noone@mail.com Analysis of Dieting study 16S data % Fri Sep 7 05:46:18 2018

(1.1.1.4.3) Plots of Abundance.

Plots are shown with relation to various combinations of meta data variables and in different graphical representations. Lots of plots here.

(1.1.1.4.3.2) Iterating over all combinations of grouping variables
(1.1.1.4.3.2.1) Grouping variables Sample.type,visit
(1.1.1.4.3.2.2) Iterating over Abundance. profile sorting order
(1.1.1.4.3.2.2.1) Abundance. profile sorting order: average abundance
(1.1.1.4.3.2.2.2) Iterating over dodged vs faceted bars

The same data are shown in multiple combinations of graphical representations. This is the same data, but each plot highlights slightly different aspects of it. It is not likely that you will need every plot - pick only what you need.

(1.1.1.4.3.2.2.2.1) faceted plots. Iterating over orientation and, optionally, scaling
(1.1.1.4.3.2.2.2.1.1) Abundance. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.1.1.4.3.2.2.2.1.1.0) Table 62. Data table used for plots. Data grouped by Sample.type,visit. Showing only 200 first rows. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.1.1.4.3.2.2.2.1.1.0-3234afa226c.1.1.1.4.3.2.2.2.1.1.csv

.record.id Sample.type visit feature Abundance
SM1 patient 1 Bacteroides.Otu0001 3.325e-02
SM10 patient 3 Bacteroides.Otu0001 0.000e+00
SM100 patient 4 Bacteroides.Otu0001 7.692e-05
SM11 patient 2 Bacteroides.Otu0001 2.280e-01
SM12 patient 1 Bacteroides.Otu0001 2.363e-01
SM13 patient 1 Bacteroides.Otu0001 2.143e-02
SM14 patient 1 Bacteroides.Otu0001 0.000e+00
SM15 control 1 Bacteroides.Otu0001 3.935e-02
SM16 patient 4 Bacteroides.Otu0001 3.835e-02
SM17 patient 1 Bacteroides.Otu0001 1.738e-01
SM18 patient 2 Bacteroides.Otu0001 1.343e-03
SM19 patient 2 Bacteroides.Otu0001 3.656e-02
SM2 patient 1 Bacteroides.Otu0001 7.129e-03
SM20 control 1 Bacteroides.Otu0001 5.936e-02
SM21 patient 1 Bacteroides.Otu0001 9.063e-02
SM22 patient 1 Bacteroides.Otu0001 1.800e-01
SM23 patient 2 Bacteroides.Otu0001 2.207e-01
SM24 patient 1 Bacteroides.Otu0001 6.084e-02
SM25 patient 4 Bacteroides.Otu0001 0.000e+00
SM26 control 1 Bacteroides.Otu0001 5.819e-02
SM28 control 1 Bacteroides.Otu0001 1.415e-01
SM29 patient 3 Bacteroides.Otu0001 1.015e-01
SM3 patient 2 Bacteroides.Otu0001 5.679e-02
SM30 patient 4 Bacteroides.Otu0001 4.615e-02
SM31 control 2 Bacteroides.Otu0001 3.883e-02
SM33 patient 1 Bacteroides.Otu0001 0.000e+00
SM35 control 1 Bacteroides.Otu0001 1.546e-02
SM36 patient 4 Bacteroides.Otu0001 0.000e+00
SM37 control 1 Bacteroides.Otu0001 8.035e-02
SM38 patient 2 Bacteroides.Otu0001 2.849e-01
SM39 patient 1 Bacteroides.Otu0001 1.512e-01
SM40 patient 4 Bacteroides.Otu0001 1.767e-02
SM41 patient 1 Bacteroides.Otu0001 4.380e-02
SM42 patient 4 Bacteroides.Otu0001 2.641e-01
SM43 patient 4 Bacteroides.Otu0001 1.241e-01
SM44 control 1 Bacteroides.Otu0001 5.478e-04
SM45 patient 2 Bacteroides.Otu0001 0.000e+00
SM48 control 1 Bacteroides.Otu0001 6.268e-02
SM49 patient 1 Bacteroides.Otu0001 1.179e-01
SM5 patient 3 Bacteroides.Otu0001 2.741e-01
SM50 patient 3 Bacteroides.Otu0001 0.000e+00
SM51 patient 4 Bacteroides.Otu0001 2.826e-01
SM52 patient 1 Bacteroides.Otu0001 5.829e-02
SM53 patient 2 Bacteroides.Otu0001 2.368e-01
SM54 patient 3 Bacteroides.Otu0001 0.000e+00
SM55 control 1 Bacteroides.Otu0001 2.798e-02
SM56 patient 2 Bacteroides.Otu0001 0.000e+00
SM57 patient 1 Bacteroides.Otu0001 1.037e-01
SM58 patient 2 Bacteroides.Otu0001 1.620e-04
SM59 patient 3 Bacteroides.Otu0001 3.745e-03
SM60 patient 3 Bacteroides.Otu0001 2.447e-01
SM62 patient 1 Bacteroides.Otu0001 5.347e-01
SM63 control 1 Bacteroides.Otu0001 8.649e-02
SM64 patient 2 Bacteroides.Otu0001 3.508e-01
SM65 patient 3 Bacteroides.Otu0001 8.092e-02
SM66 control 1 Bacteroides.Otu0001 1.585e-01
SM67 patient 4 Bacteroides.Otu0001 2.186e-01
SM68 patient 4 Bacteroides.Otu0001 0.000e+00
SM69 patient 4 Bacteroides.Otu0001 1.655e-01
SM7 control 1 Bacteroides.Otu0001 4.313e-02
SM70 control 1 Bacteroides.Otu0001 1.567e-02
SM71 patient 3 Bacteroides.Otu0001 2.788e-01
SM72 control 1 Bacteroides.Otu0001 1.323e-03
SM73 patient 1 Bacteroides.Otu0001 1.891e-01
SM74 control 2 Bacteroides.Otu0001 5.565e-02
SM75 patient 3 Bacteroides.Otu0001 0.000e+00
SM76 control 1 Bacteroides.Otu0001 2.751e-02
SM77 patient 2 Bacteroides.Otu0001 2.034e-01
SM79 patient 2 Bacteroides.Otu0001 2.642e-02
SM8 patient 1 Bacteroides.Otu0001 5.265e-02
SM81 control 1 Bacteroides.Otu0001 0.000e+00
SM82 patient 4 Bacteroides.Otu0001 1.052e-02
SM83 patient 1 Bacteroides.Otu0001 0.000e+00
SM84 patient 1 Bacteroides.Otu0001 1.247e-01
SM86 patient 2 Bacteroides.Otu0001 0.000e+00
SM87 patient 1 Bacteroides.Otu0001 1.941e-01
SM88 patient 2 Bacteroides.Otu0001 2.302e-02
SM89 control 1 Bacteroides.Otu0001 0.000e+00
SM9 patient 2 Bacteroides.Otu0001 3.497e-02
SM90 patient 2 Bacteroides.Otu0001 3.713e-02
SM91 patient 3 Bacteroides.Otu0001 1.254e-01
SM92 patient 3 Bacteroides.Otu0001 0.000e+00
SM93 patient 1 Bacteroides.Otu0001 3.120e-01
SM95 control 1 Bacteroides.Otu0001 1.492e-01
SM96 patient 1 Bacteroides.Otu0001 0.000e+00
SM98 patient 3 Bacteroides.Otu0001 3.648e-02
SM99 patient 3 Bacteroides.Otu0001 4.305e-02
SM1 patient 1 Bacteroides.Otu2520 1.003e-01
SM10 patient 3 Bacteroides.Otu2520 0.000e+00
SM100 patient 4 Bacteroides.Otu2520 0.000e+00
SM11 patient 2 Bacteroides.Otu2520 1.344e-01
SM12 patient 1 Bacteroides.Otu2520 1.504e-01
SM13 patient 1 Bacteroides.Otu2520 1.473e-02
SM14 patient 1 Bacteroides.Otu2520 3.786e-04
SM15 control 1 Bacteroides.Otu2520 1.756e-01
SM16 patient 4 Bacteroides.Otu2520 0.000e+00
SM17 patient 1 Bacteroides.Otu2520 1.862e-02
SM18 patient 2 Bacteroides.Otu2520 1.074e-02
SM19 patient 2 Bacteroides.Otu2520 9.255e-04
SM2 patient 1 Bacteroides.Otu2520 1.638e-01
SM20 control 1 Bacteroides.Otu2520 2.417e-01
SM21 patient 1 Bacteroides.Otu2520 4.540e-03
SM22 patient 1 Bacteroides.Otu2520 2.610e-02
SM23 patient 2 Bacteroides.Otu2520 0.000e+00
SM24 patient 1 Bacteroides.Otu2520 5.531e-03
SM25 patient 4 Bacteroides.Otu2520 3.053e-01
SM26 control 1 Bacteroides.Otu2520 4.378e-02
SM28 control 1 Bacteroides.Otu2520 0.000e+00
SM29 patient 3 Bacteroides.Otu2520 0.000e+00
SM3 patient 2 Bacteroides.Otu2520 5.657e-04
SM30 patient 4 Bacteroides.Otu2520 3.250e-04
SM31 control 2 Bacteroides.Otu2520 1.173e-02
SM33 patient 1 Bacteroides.Otu2520 7.120e-02
SM35 control 1 Bacteroides.Otu2520 1.330e-01
SM36 patient 4 Bacteroides.Otu2520 0.000e+00
SM37 control 1 Bacteroides.Otu2520 3.158e-02
SM38 patient 2 Bacteroides.Otu2520 9.696e-02
SM39 patient 1 Bacteroides.Otu2520 8.620e-03
SM40 patient 4 Bacteroides.Otu2520 5.920e-02
SM41 patient 1 Bacteroides.Otu2520 1.440e-01
SM42 patient 4 Bacteroides.Otu2520 1.665e-04
SM43 patient 4 Bacteroides.Otu2520 3.957e-02
SM44 control 1 Bacteroides.Otu2520 1.369e-03
SM45 patient 2 Bacteroides.Otu2520 0.000e+00
SM48 control 1 Bacteroides.Otu2520 1.951e-02
SM49 patient 1 Bacteroides.Otu2520 1.715e-01
SM5 patient 3 Bacteroides.Otu2520 0.000e+00
SM50 patient 3 Bacteroides.Otu2520 0.000e+00
SM51 patient 4 Bacteroides.Otu2520 3.368e-02
SM52 patient 1 Bacteroides.Otu2520 2.179e-04
SM53 patient 2 Bacteroides.Otu2520 7.192e-05
SM54 patient 3 Bacteroides.Otu2520 2.426e-01
SM55 control 1 Bacteroides.Otu2520 1.289e-03
SM56 patient 2 Bacteroides.Otu2520 9.465e-03
SM57 patient 1 Bacteroides.Otu2520 0.000e+00
SM58 patient 2 Bacteroides.Otu2520 3.239e-04
SM59 patient 3 Bacteroides.Otu2520 2.996e-03
SM60 patient 3 Bacteroides.Otu2520 5.548e-02
SM62 patient 1 Bacteroides.Otu2520 1.525e-02
SM63 control 1 Bacteroides.Otu2520 4.324e-02
SM64 patient 2 Bacteroides.Otu2520 9.297e-03
SM65 patient 3 Bacteroides.Otu2520 0.000e+00
SM66 control 1 Bacteroides.Otu2520 9.282e-02
SM67 patient 4 Bacteroides.Otu2520 0.000e+00
SM68 patient 4 Bacteroides.Otu2520 0.000e+00
SM69 patient 4 Bacteroides.Otu2520 1.197e-02
SM7 control 1 Bacteroides.Otu2520 0.000e+00
SM70 control 1 Bacteroides.Otu2520 5.961e-03
SM71 patient 3 Bacteroides.Otu2520 2.162e-02
SM72 control 1 Bacteroides.Otu2520 0.000e+00
SM73 patient 1 Bacteroides.Otu2520 5.047e-04
SM74 control 2 Bacteroides.Otu2520 0.000e+00
SM75 patient 3 Bacteroides.Otu2520 2.037e-03
SM76 control 1 Bacteroides.Otu2520 1.085e-02
SM77 patient 2 Bacteroides.Otu2520 8.359e-02
SM79 patient 2 Bacteroides.Otu2520 1.576e-02
SM8 patient 1 Bacteroides.Otu2520 0.000e+00
SM81 control 1 Bacteroides.Otu2520 0.000e+00
SM82 patient 4 Bacteroides.Otu2520 3.568e-01
SM83 patient 1 Bacteroides.Otu2520 0.000e+00
SM84 patient 1 Bacteroides.Otu2520 2.912e-03
SM86 patient 2 Bacteroides.Otu2520 0.000e+00
SM87 patient 1 Bacteroides.Otu2520 4.566e-02
SM88 patient 2 Bacteroides.Otu2520 1.604e-01
SM89 control 1 Bacteroides.Otu2520 0.000e+00
SM9 patient 2 Bacteroides.Otu2520 5.636e-02
SM90 patient 2 Bacteroides.Otu2520 2.558e-02
SM91 patient 3 Bacteroides.Otu2520 8.567e-02
SM92 patient 3 Bacteroides.Otu2520 9.504e-03
SM93 patient 1 Bacteroides.Otu2520 4.034e-04
SM95 control 1 Bacteroides.Otu2520 6.748e-02
SM96 patient 1 Bacteroides.Otu2520 4.602e-01
SM98 patient 3 Bacteroides.Otu2520 9.832e-04
SM99 patient 3 Bacteroides.Otu2520 4.757e-04
SM1 patient 1 Faecalibacterium.Otu0067 6.148e-03
SM10 patient 3 Faecalibacterium.Otu0067 1.051e-01
SM100 patient 4 Faecalibacterium.Otu0067 6.200e-02
SM11 patient 2 Faecalibacterium.Otu0067 1.893e-02
SM12 patient 1 Faecalibacterium.Otu0067 4.471e-03
SM13 patient 1 Faecalibacterium.Otu0067 8.929e-04
SM14 patient 1 Faecalibacterium.Otu0067 4.014e-02
SM15 control 1 Faecalibacterium.Otu0067 2.045e-02
SM16 patient 4 Faecalibacterium.Otu0067 1.237e-01
SM17 patient 1 Faecalibacterium.Otu0067 4.137e-04
SM18 patient 2 Faecalibacterium.Otu0067 3.022e-03
SM19 patient 2 Faecalibacterium.Otu0067 2.920e-01
SM2 patient 1 Faecalibacterium.Otu0067 9.919e-04
SM20 control 1 Faecalibacterium.Otu0067 8.058e-04
SM21 patient 1 Faecalibacterium.Otu0067 1.093e-02
SM22 patient 1 Faecalibacterium.Otu0067 4.607e-03
SM23 patient 2 Faecalibacterium.Otu0067 0.000e+00
SM24 patient 1 Faecalibacterium.Otu0067 1.839e-02
SM25 patient 4 Faecalibacterium.Otu0067 6.406e-02
SM26 control 1 Faecalibacterium.Otu0067 6.205e-03
SM28 control 1 Faecalibacterium.Otu0067 1.307e-01
SM29 patient 3 Faecalibacterium.Otu0067 3.342e-03
SM3 patient 2 Faecalibacterium.Otu0067 3.733e-03
SM30 patient 4 Faecalibacterium.Otu0067 1.202e-02
SM31 control 2 Faecalibacterium.Otu0067 2.427e-03
SM33 patient 1 Faecalibacterium.Otu0067 0.000e+00

(1.1.1.4.3.2.2.2.1.1.1) Widget 65. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Stacked Bar Chart. Data grouped by Sample.type,visit. Click to see HTML widget file in full window: ./1.1.1.4.3.2.2.2.1.1.1-32349638518Dynamic.Pivot.Table.html

(1.1.1.4.3.2.2.2.1.1.1) Widget 66. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Table Barchart. Data grouped by Sample.type,visit. Click to see HTML widget file in full window: ./1.1.1.4.3.2.2.2.1.1.1-3235e0bf528Dynamic.Pivot.Table.html

(1.1.1.4.3.2.2.2.1.1.1) Table 63. Summary table. Data grouped by Sample.type,visit. Showing only 200 first rows. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.1.1.4.3.2.2.2.1.1.1-3231e3485b1.1.1.1.4.3.2.2.2.1.1.csv

feature Sample.type visit mean sd median incidence
Bacteroides.Otu0001 control 1 5.373e-02 5.181e-02 4.124e-02 0.88889
Bacteroides.Otu0001 control 2 4.724e-02 1.189e-02 4.724e-02 1.00000
Bacteroides.Otu0001 patient 1 1.168e-01 1.255e-01 9.063e-02 0.82609
Bacteroides.Otu0001 patient 2 1.024e-01 1.205e-01 3.656e-02 0.82353
Bacteroides.Otu0001 patient 3 8.491e-02 1.066e-01 3.976e-02 0.64286
Bacteroides.Otu0001 patient 4 8.982e-02 1.078e-01 3.835e-02 0.76923
Bacteroides.Otu2520 control 1 4.824e-02 7.012e-02 1.518e-02 0.72222
Bacteroides.Otu2520 control 2 5.866e-03 8.295e-03 5.866e-03 0.50000
Bacteroides.Otu2520 patient 1 6.108e-02 1.054e-01 1.473e-02 0.86957
Bacteroides.Otu2520 patient 2 3.555e-02 5.188e-02 9.465e-03 0.82353
Bacteroides.Otu2520 patient 3 3.010e-02 6.631e-02 1.510e-03 0.64286
Bacteroides.Otu2520 patient 4 6.208e-02 1.214e-01 3.250e-04 0.61538
Faecalibacterium.Otu0067 control 1 2.757e-02 3.097e-02 2.053e-02 0.94444
Faecalibacterium.Otu0067 control 2 2.134e-02 2.675e-02 2.134e-02 1.00000
Faecalibacterium.Otu0067 patient 1 1.768e-02 1.932e-02 1.166e-02 0.95652
Faecalibacterium.Otu0067 patient 2 4.572e-02 9.221e-02 9.465e-03 0.88235
Faecalibacterium.Otu0067 patient 3 2.381e-02 2.918e-02 1.341e-02 0.92857
Faecalibacterium.Otu0067 patient 4 4.894e-02 5.938e-02 2.672e-02 1.00000
Prevotella.Otu1987 control 1 6.034e-02 1.115e-01 0.000e+00 0.33333
Prevotella.Otu1987 control 2 0.000e+00 0.000e+00 0.000e+00 0.00000
Prevotella.Otu1987 patient 1 3.124e-02 9.994e-02 0.000e+00 0.26087
Prevotella.Otu1987 patient 2 3.192e-02 7.957e-02 0.000e+00 0.47059
Prevotella.Otu1987 patient 3 1.874e-02 6.410e-02 0.000e+00 0.21429
Prevotella.Otu1987 patient 4 4.165e-05 8.770e-05 0.000e+00 0.30769
Bacteroides.Otu0848 control 1 1.065e-02 2.194e-02 1.240e-03 0.66667
Bacteroides.Otu0848 control 2 4.248e-03 6.007e-03 4.248e-03 0.50000
Bacteroides.Otu0848 patient 1 2.252e-02 3.495e-02 6.558e-03 0.86957
Bacteroides.Otu0848 patient 2 1.478e-02 2.389e-02 2.060e-03 0.76471
Bacteroides.Otu0848 patient 3 7.368e-02 1.374e-01 7.264e-03 0.64286
Bacteroides.Otu0848 patient 4 3.335e-02 5.821e-02 1.387e-03 0.84615
Bacteroides.Otu2038 control 1 1.297e-02 3.185e-02 2.747e-03 0.77778
Bacteroides.Otu2038 control 2 2.898e-03 2.382e-03 2.898e-03 1.00000
Bacteroides.Otu2038 patient 1 2.623e-02 6.465e-02 3.601e-03 0.86957
Bacteroides.Otu2038 patient 2 1.914e-02 4.313e-02 3.327e-03 0.76471
Bacteroides.Otu2038 patient 3 2.982e-02 8.896e-02 3.932e-03 0.64286
Bacteroides.Otu2038 patient 4 4.044e-02 8.116e-02 1.341e-03 0.69231
Parabacteroides.Otu1736 control 1 4.727e-03 5.893e-03 3.900e-03 0.83333
Parabacteroides.Otu1736 control 2 8.764e-03 5.913e-03 8.764e-03 1.00000
Parabacteroides.Otu1736 patient 1 2.509e-02 9.916e-02 1.328e-04 0.56522
Parabacteroides.Otu1736 patient 2 4.847e-02 1.628e-01 0.000e+00 0.47059
Parabacteroides.Otu1736 patient 3 2.566e-02 4.900e-02 2.089e-04 0.50000
Parabacteroides.Otu1736 patient 4 1.245e-03 2.634e-03 0.000e+00 0.38462
Bacteroides.Otu2654 control 1 5.269e-03 8.442e-03 5.437e-04 0.72222
Bacteroides.Otu2654 control 2 0.000e+00 0.000e+00 0.000e+00 0.00000
Bacteroides.Otu2654 patient 1 4.783e-02 9.677e-02 1.076e-02 0.78261
Bacteroides.Otu2654 patient 2 6.019e-03 1.456e-02 8.251e-04 0.64706
Bacteroides.Otu2654 patient 3 7.518e-03 2.057e-02 3.516e-04 0.71429
Bacteroides.Otu2654 patient 4 8.816e-03 1.555e-02 6.232e-04 0.76923
Bacteroides.Otu2065 control 1 7.046e-03 1.378e-02 0.000e+00 0.33333
Bacteroides.Otu2065 control 2 0.000e+00 0.000e+00 0.000e+00 0.00000
Bacteroides.Otu2065 patient 1 2.112e-02 8.207e-02 0.000e+00 0.21739
Bacteroides.Otu2065 patient 2 6.964e-03 2.745e-02 0.000e+00 0.23529
Bacteroides.Otu2065 patient 3 3.925e-02 1.403e-01 0.000e+00 0.21429
Bacteroides.Otu2065 patient 4 1.719e-02 3.186e-02 0.000e+00 0.38462
Bacteroides.Otu0863 control 1 7.645e-03 8.815e-03 6.083e-03 0.77778
Bacteroides.Otu0863 control 2 6.250e-02 8.839e-02 6.250e-02 0.50000
Bacteroides.Otu0863 patient 1 3.229e-02 5.790e-02 1.493e-02 0.86957
Bacteroides.Otu0863 patient 2 1.189e-02 3.395e-02 3.239e-04 0.58824
Bacteroides.Otu0863 patient 3 5.235e-03 7.618e-03 8.642e-04 0.57143
Bacteroides.Otu0863 patient 4 1.266e-02 2.901e-02 6.500e-04 0.61538
Bacteroides.Otu2431 control 1 1.752e-02 2.195e-02 6.948e-03 0.72222
Bacteroides.Otu2431 control 2 1.133e-02 1.602e-02 1.133e-02 0.50000
Bacteroides.Otu2431 patient 1 1.553e-02 2.341e-02 7.537e-03 0.82609
Bacteroides.Otu2431 patient 2 1.552e-02 1.948e-02 1.151e-03 0.76471
Bacteroides.Otu2431 patient 3 1.000e-02 1.290e-02 3.306e-03 0.78571
Bacteroides.Otu2431 patient 4 2.651e-02 3.608e-02 8.739e-03 0.76923
Bacteroides.Otu0929 control 1 7.901e-03 9.570e-03 4.583e-03 0.83333
Bacteroides.Otu0929 control 2 1.136e-03 6.813e-04 1.136e-03 1.00000
Bacteroides.Otu0929 patient 1 2.297e-02 4.878e-02 3.724e-03 0.73913
Bacteroides.Otu0929 patient 2 1.557e-02 2.119e-02 7.838e-03 0.70588
Bacteroides.Otu0929 patient 3 1.534e-02 2.263e-02 4.461e-03 0.64286
Bacteroides.Otu0929 patient 4 1.128e-02 1.351e-02 1.271e-02 0.61538
Bacteroides.Otu1201 control 1 3.699e-03 4.973e-03 2.154e-03 0.72222
Bacteroides.Otu1201 control 2 2.104e-02 2.975e-02 2.104e-02 0.50000
Bacteroides.Otu1201 patient 1 1.796e-02 4.252e-02 4.950e-03 0.82609
Bacteroides.Otu1201 patient 2 3.298e-03 5.159e-03 9.464e-04 0.64706
Bacteroides.Otu1201 patient 3 7.161e-03 1.720e-02 0.000e+00 0.42857
Bacteroides.Otu1201 patient 4 3.302e-02 1.068e-01 0.000e+00 0.46154
Bacteroides.Otu0786 control 1 1.213e-03 2.598e-03 0.000e+00 0.33333
Bacteroides.Otu0786 control 2 1.618e-03 2.288e-03 1.618e-03 0.50000
Bacteroides.Otu0786 patient 1 1.362e-02 5.207e-02 0.000e+00 0.47826
Bacteroides.Otu0786 patient 2 2.502e-02 7.930e-02 0.000e+00 0.47059
Bacteroides.Otu0786 patient 3 1.140e-02 2.458e-02 0.000e+00 0.35714
Bacteroides.Otu0786 patient 4 1.288e-02 3.648e-02 0.000e+00 0.30769
Alistipes.Otu2508 control 1 1.852e-02 2.951e-02 4.785e-03 0.66667
Alistipes.Otu2508 control 2 5.057e-02 7.151e-02 5.057e-02 0.50000
Alistipes.Otu2508 patient 1 1.774e-02 4.589e-02 5.195e-04 0.52174
Alistipes.Otu2508 patient 2 7.004e-03 1.243e-02 0.000e+00 0.35294
Alistipes.Otu2508 patient 3 4.125e-03 1.088e-02 0.000e+00 0.35714
Alistipes.Otu2508 patient 4 4.789e-03 9.796e-03 0.000e+00 0.38462
Bacteroides.Otu2625 control 1 6.692e-03 1.678e-02 6.631e-04 0.66667
Bacteroides.Otu2625 control 2 4.248e-03 6.007e-03 4.248e-03 0.50000
Bacteroides.Otu2625 patient 1 1.951e-02 4.503e-02 6.678e-04 0.65217
Bacteroides.Otu2625 patient 2 6.004e-03 1.190e-02 0.000e+00 0.47059
Bacteroides.Otu2625 patient 3 1.810e-02 6.380e-02 0.000e+00 0.42857
Bacteroides.Otu2625 patient 4 6.002e-03 1.671e-02 0.000e+00 0.46154
Lactobacillus.Otu1332 control 1 0.000e+00 0.000e+00 0.000e+00 0.00000
Lactobacillus.Otu1332 control 2 0.000e+00 0.000e+00 0.000e+00 0.00000
Lactobacillus.Otu1332 patient 1 6.648e-05 1.999e-04 0.000e+00 0.13043
Lactobacillus.Otu1332 patient 2 5.866e-02 2.418e-01 0.000e+00 0.11765
Lactobacillus.Otu1332 patient 3 3.771e-04 1.267e-03 0.000e+00 0.14286
Lactobacillus.Otu1332 patient 4 2.476e-05 8.927e-05 0.000e+00 0.07692
Blautia.Otu2475 control 1 1.814e-02 4.375e-02 7.955e-03 1.00000
Blautia.Otu2475 control 2 1.313e-02 1.800e-02 1.313e-02 1.00000
Blautia.Otu2475 patient 1 6.579e-03 9.572e-03 2.046e-03 0.91304
Blautia.Otu2475 patient 2 8.246e-03 1.284e-02 2.182e-03 0.82353
Blautia.Otu2475 patient 3 1.626e-02 1.876e-02 1.049e-02 1.00000
Blautia.Otu2475 patient 4 1.008e-02 1.295e-02 3.353e-03 1.00000
Clostridium_XI.Otu1804 control 1 8.144e-03 1.014e-02 5.866e-03 0.94444
Clostridium_XI.Otu1804 control 2 9.628e-03 6.752e-03 9.628e-03 1.00000
Clostridium_XI.Otu1804 patient 1 1.197e-02 2.513e-02 2.170e-03 0.82609
Clostridium_XI.Otu1804 patient 2 1.102e-02 3.350e-02 1.004e-03 0.76471
Clostridium_XI.Otu1804 patient 3 6.055e-03 8.430e-03 1.934e-03 0.92857
Clostridium_XI.Otu1804 patient 4 2.040e-02 3.328e-02 4.832e-03 1.00000
Bacteroides.Otu0069 control 1 6.746e-03 6.781e-03 4.877e-03 0.77778
Bacteroides.Otu0069 control 2 6.721e-03 2.068e-03 6.721e-03 1.00000
Bacteroides.Otu0069 patient 1 1.411e-02 1.696e-02 1.076e-02 0.82609
Bacteroides.Otu0069 patient 2 1.321e-02 1.506e-02 3.713e-03 0.76471
Bacteroides.Otu0069 patient 3 1.110e-02 1.631e-02 2.610e-03 0.64286
Bacteroides.Otu0069 patient 4 8.984e-03 1.193e-02 1.757e-03 0.69231
Bacteroides.Otu2765 control 1 4.704e-03 7.441e-03 1.156e-03 0.72222
Bacteroides.Otu2765 control 2 1.011e-03 1.430e-03 1.011e-03 0.50000
Bacteroides.Otu2765 patient 1 1.268e-02 1.724e-02 5.045e-03 0.91304
Bacteroides.Otu2765 patient 2 8.741e-03 1.310e-02 1.503e-03 0.70588
Bacteroides.Otu2765 patient 3 1.885e-02 2.845e-02 4.255e-04 0.57143
Bacteroides.Otu2765 patient 4 1.183e-02 1.842e-02 8.125e-04 0.76923
Bacteroides.Otu0661 control 1 7.332e-03 9.733e-03 4.161e-03 0.66667
Bacteroides.Otu0661 control 2 1.339e-03 9.673e-04 1.339e-03 1.00000
Bacteroides.Otu0661 patient 1 1.387e-02 2.320e-02 3.919e-03 0.73913
Bacteroides.Otu0661 patient 2 1.186e-02 1.657e-02 3.300e-03 0.70588
Bacteroides.Otu0661 patient 3 1.011e-02 1.377e-02 2.137e-03 0.50000
Bacteroides.Otu0661 patient 4 7.730e-03 1.025e-02 1.385e-03 0.61538
Enterococcus.Otu1019 control 1 3.118e-03 1.311e-02 0.000e+00 0.16667
Enterococcus.Otu1019 control 2 3.437e-03 4.861e-03 3.437e-03 0.50000
Enterococcus.Otu1019 patient 1 3.367e-03 1.493e-02 0.000e+00 0.26087
Enterococcus.Otu1019 patient 2 4.210e-02 1.720e-01 0.000e+00 0.41176
Enterococcus.Otu1019 patient 3 2.699e-04 5.710e-04 0.000e+00 0.28571
Enterococcus.Otu1019 patient 4 1.910e-04 6.012e-04 0.000e+00 0.15385
Ruminococcus.Otu1859 control 1 3.248e-02 5.826e-02 6.379e-03 0.66667
Ruminococcus.Otu1859 control 2 5.838e-02 8.085e-02 5.838e-02 1.00000
Ruminococcus.Otu1859 patient 1 1.516e-03 5.680e-03 0.000e+00 0.26087
Ruminococcus.Otu1859 patient 2 5.155e-04 1.790e-03 0.000e+00 0.23529
Ruminococcus.Otu1859 patient 3 5.691e-03 2.122e-02 0.000e+00 0.14286
Ruminococcus.Otu1859 patient 4 6.578e-04 1.526e-03 0.000e+00 0.23077
Alistipes.Otu1466 control 1 1.621e-02 4.029e-02 1.998e-04 0.50000
Alistipes.Otu1466 control 2 7.811e-03 1.012e-02 7.811e-03 1.00000
Alistipes.Otu1466 patient 1 1.086e-02 1.787e-02 2.576e-03 0.52174
Alistipes.Otu1466 patient 2 1.322e-02 3.707e-02 0.000e+00 0.35294
Alistipes.Otu1466 patient 3 2.084e-03 4.903e-03 0.000e+00 0.35714
Alistipes.Otu1466 patient 4 1.656e-03 3.001e-03 0.000e+00 0.38462
Erysipelotrichaceae_incertae_sedis.Otu0818 control 1 6.704e-04 1.343e-03 7.077e-05 0.50000
Erysipelotrichaceae_incertae_sedis.Otu0818 control 2 8.955e-04 1.223e-04 8.955e-04 1.00000
Erysipelotrichaceae_incertae_sedis.Otu0818 patient 1 1.994e-02 8.001e-02 9.525e-04 0.69565
Erysipelotrichaceae_incertae_sedis.Otu0818 patient 2 1.488e-03 2.518e-03 3.410e-04 0.76471
Erysipelotrichaceae_incertae_sedis.Otu0818 patient 3 8.981e-03 1.397e-02 2.219e-03 1.00000
Erysipelotrichaceae_incertae_sedis.Otu0818 patient 4 1.508e-02 5.012e-02 9.325e-04 0.84615
Bacteroides.Otu0006 control 1 5.163e-03 6.317e-03 3.693e-03 0.77778
Bacteroides.Otu0006 control 2 8.955e-04 1.223e-04 8.955e-04 1.00000
Bacteroides.Otu0006 patient 1 1.051e-02 9.565e-03 7.294e-03 0.82609
Bacteroides.Otu0006 patient 2 1.063e-02 1.320e-02 5.285e-03 0.76471
Bacteroides.Otu0006 patient 3 9.002e-03 1.122e-02 5.222e-03 0.57143
Bacteroides.Otu0006 patient 4 1.226e-02 1.303e-02 9.315e-03 0.69231
Bacteroides.Otu2343 control 1 7.090e-04 1.618e-03 0.000e+00 0.38889
Bacteroides.Otu2343 control 2 6.068e-04 8.581e-04 6.068e-04 0.50000
Bacteroides.Otu2343 patient 1 7.836e-03 2.709e-02 4.426e-05 0.52174
Bacteroides.Otu2343 patient 2 1.645e-02 5.090e-02 1.028e-04 0.52941
Bacteroides.Otu2343 patient 3 7.405e-03 1.561e-02 0.000e+00 0.35714
Bacteroides.Otu2343 patient 4 1.140e-02 3.140e-02 0.000e+00 0.30769
Lachnospiracea_incertae_sedis.Otu0778 control 1 2.020e-03 2.017e-03 1.729e-03 0.77778
Lachnospiracea_incertae_sedis.Otu0778 control 2 4.255e-03 6.018e-03 4.255e-03 0.50000
Lachnospiracea_incertae_sedis.Otu0778 patient 1 1.813e-03 3.516e-03 3.708e-04 0.56522
Lachnospiracea_incertae_sedis.Otu0778 patient 2 6.233e-03 1.008e-02 1.343e-03 0.76471
Lachnospiracea_incertae_sedis.Otu0778 patient 3 6.674e-03 1.333e-02 7.028e-04 0.57143
Lachnospiracea_incertae_sedis.Otu0778 patient 4 3.192e-02 5.684e-02 9.750e-03 0.69231
Prevotella.Otu1633 control 1 4.917e-03 1.109e-02 0.000e+00 0.38889
Prevotella.Otu1633 control 2 3.273e-04 4.629e-04 3.273e-04 0.50000
Prevotella.Otu1633 patient 1 4.798e-03 1.274e-02 0.000e+00 0.43478
Prevotella.Otu1633 patient 2 2.845e-02 1.138e-01 0.000e+00 0.29412
Prevotella.Otu1633 patient 3 1.804e-04 4.922e-04 0.000e+00 0.35714
Prevotella.Otu1633 patient 4 3.356e-04 1.210e-03 0.000e+00 0.07692
Bacteroides.Otu2437 control 1 1.140e-02 2.451e-02 4.701e-04 0.66667
Bacteroides.Otu2437 control 2 9.709e-03 1.373e-02 9.709e-03 0.50000
Bacteroides.Otu2437 patient 1 3.057e-03 6.170e-03 0.000e+00 0.47826
Bacteroides.Otu2437 patient 2 8.595e-03 2.110e-02 0.000e+00 0.35294
Bacteroides.Otu2437 patient 3 3.449e-03 8.349e-03 0.000e+00 0.35714
Bacteroides.Otu2437 patient 4 1.275e-02 2.527e-02 0.000e+00 0.46154
Escherichia_Shigella.Otu2393 control 1 1.014e-02 3.951e-02 3.219e-04 0.55556
Escherichia_Shigella.Otu2393 control 2 4.045e-04 5.721e-04 4.045e-04 0.50000
Escherichia_Shigella.Otu2393 patient 1 1.408e-02 4.403e-02 0.000e+00 0.39130
Escherichia_Shigella.Otu2393 patient 2 3.576e-04 1.298e-03 0.000e+00 0.29412
Escherichia_Shigella.Otu2393 patient 3 2.305e-03 5.001e-03 3.234e-04 0.64286
Escherichia_Shigella.Otu2393 patient 4 7.439e-03 1.716e-02 8.323e-05 0.53846
Prevotella.Otu1994 control 1 2.627e-02 6.026e-02 0.000e+00 0.22222
Prevotella.Otu1994 control 2 0.000e+00 0.000e+00 0.000e+00 0.00000
Prevotella.Otu1994 patient 1 3.362e-03 1.356e-02 0.000e+00 0.08696
Prevotella.Otu1994 patient 2 4.061e-03 1.675e-02 0.000e+00 0.05882
Prevotella.Otu1994 patient 3 4.960e-04 1.833e-03 0.000e+00 0.14286
Prevotella.Otu1994 patient 4 2.352e-06 8.481e-06 0.000e+00 0.07692
Bacteroides.Otu0480 control 1 1.057e-02 3.008e-02 0.000e+00 0.33333
Bacteroides.Otu0480 control 2 3.236e-02 4.577e-02 3.236e-02 0.50000

(1.1.1.4.3.2.2.2.1.1.1) Figure 194. Abundance. Data grouped by Sample.type,visit. bar_stacked plot. Image file: plots/323100ecb64.svg.

(1.1.1.4.3.2.2.2.1.1.1) Figure 195. Abundance. Data grouped by Sample.type,visit. bar (sample mean) plot. Image file: plots/3233a2fa2a3.svg.

(1.1.1.4.3.2.2.2.1.1.1) Figure 196. Abundance. Data grouped by Sample.type,visit. violin plot. Image file: plots/3231eee42e7.svg.

(1.1.1.4.3.2.2.2.1.1.1) Figure 197. Abundance. Data grouped by Sample.type,visit. boxplot plot. Image file: plots/32328653ce6.svg.

(1.1.1.4.3.2.2.2.1.2) Abundance. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.1.1.4.3.2.2.2.1.2.1) Figure 198. Abundance. Data grouped by Sample.type,visit. bar (sample mean) plot. Image file: plots/32331f28f16.svg.

(1.1.1.4.3.2.2.2.1.2.1) Figure 199. Abundance. Data grouped by Sample.type,visit. violin plot. Image file: plots/323391c1196.svg.

(1.1.1.4.3.2.2.2.1.2.1) Figure 200. Abundance. Data grouped by Sample.type,visit. boxplot plot. Image file: plots/3235d49b5fe.svg.

(1.1.1.4.3.2.2.2.2) dodged plots. Iterating over orientation and, optionally, scaling
(1.1.1.4.3.2.2.2.2.1) Abundance. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.1.1.4.3.2.2.2.2.1.1) Figure 201. Abundance. Data grouped by Sample.type,visit. bar (sample mean) plot. Image file: plots/32346bd8ca3.svg.

(1.1.1.4.3.2.2.2.2.1.1) Figure 202. Abundance. Data grouped by Sample.type,visit. violin plot. Image file: plots/323178a5fad.svg.

(1.1.1.4.3.2.2.2.2.1.1) Figure 203. Abundance. Data grouped by Sample.type,visit. boxplot plot. Image file: plots/323624018a4.svg.

(1.1.1.4.3.2.2.2.2.2) Abundance. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.1.1.4.3.2.2.2.2.2.1) Figure 204. Abundance. Data grouped by Sample.type,visit. bar (sample mean) plot. Image file: plots/32319f5b08d.svg.

(1.1.1.4.3.2.2.2.2.2.1) Figure 205. Abundance. Data grouped by Sample.type,visit. violin plot. Image file: plots/3239bd6ad9.svg.

(1.1.1.4.3.2.2.2.2.2.1) Figure 206. Abundance. Data grouped by Sample.type,visit. boxplot plot. Image file: plots/32343504bf1.svg.

(1.1.1.4.3.2.3) Grouping variables Sample.type.Drug.Before,visit
(1.1.1.4.3.2.4) Iterating over Abundance. profile sorting order
(1.1.1.4.3.2.4.1) Abundance. profile sorting order: average abundance
(1.1.1.4.3.2.4.2) Iterating over dodged vs faceted bars

The same data are shown in multiple combinations of graphical representations. This is the same data, but each plot highlights slightly different aspects of it. It is not likely that you will need every plot - pick only what you need.

(1.1.1.4.3.2.4.2.1) faceted plots. Iterating over orientation and, optionally, scaling
(1.1.1.4.3.2.4.2.1.1) Abundance. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.1.1.4.3.2.4.2.1.1.0) Table 64. Data table used for plots. Data grouped by Sample.type.Drug.Before,visit. Showing only 200 first rows. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.1.1.4.3.2.4.2.1.1.0-3232a14e04a.1.1.1.4.3.2.4.2.1.1.csv

.record.id Sample.type.Drug.Before visit feature Abundance
SM1 patient TRUE . 1 Bacteroides.Otu0001 3.325e-02
SM10 patient TRUE . 3 Bacteroides.Otu0001 0.000e+00
SM100 patient TRUE . 4 Bacteroides.Otu0001 7.692e-05
SM11 patient TRUE . 2 Bacteroides.Otu0001 2.280e-01
SM12 patient TRUE . 1 Bacteroides.Otu0001 2.363e-01
SM13 patient FALSE . 1 Bacteroides.Otu0001 2.143e-02
SM14 patient FALSE . 1 Bacteroides.Otu0001 0.000e+00
SM15 1 1 Bacteroides.Otu0001 3.935e-02
SM16 patient FALSE . 4 Bacteroides.Otu0001 3.835e-02
SM17 patient TRUE . 1 Bacteroides.Otu0001 1.738e-01
SM18 patient FALSE . 2 Bacteroides.Otu0001 1.343e-03
SM19 patient FALSE . 2 Bacteroides.Otu0001 3.656e-02
SM2 patient FALSE . 1 Bacteroides.Otu0001 7.129e-03
SM20 1 1 Bacteroides.Otu0001 5.936e-02
SM21 patient FALSE . 1 Bacteroides.Otu0001 9.063e-02
SM22 patient TRUE . 1 Bacteroides.Otu0001 1.800e-01
SM23 patient TRUE . 2 Bacteroides.Otu0001 2.207e-01
SM24 patient FALSE . 1 Bacteroides.Otu0001 6.084e-02
SM25 patient FALSE . 4 Bacteroides.Otu0001 0.000e+00
SM26 1 1 Bacteroides.Otu0001 5.819e-02
SM28 1 1 Bacteroides.Otu0001 1.415e-01
SM29 patient TRUE . 3 Bacteroides.Otu0001 1.015e-01
SM3 patient TRUE . 2 Bacteroides.Otu0001 5.679e-02
SM30 patient TRUE . 4 Bacteroides.Otu0001 4.615e-02
SM31 1 2 Bacteroides.Otu0001 3.883e-02
SM33 patient TRUE . 1 Bacteroides.Otu0001 0.000e+00
SM35 1 1 Bacteroides.Otu0001 1.546e-02
SM36 patient FALSE . 4 Bacteroides.Otu0001 0.000e+00
SM37 1 1 Bacteroides.Otu0001 8.035e-02
SM38 patient TRUE . 2 Bacteroides.Otu0001 2.849e-01
SM39 patient FALSE . 1 Bacteroides.Otu0001 1.512e-01
SM40 patient FALSE . 4 Bacteroides.Otu0001 1.767e-02
SM41 patient TRUE . 1 Bacteroides.Otu0001 4.380e-02
SM42 patient FALSE . 4 Bacteroides.Otu0001 2.641e-01
SM43 patient TRUE . 4 Bacteroides.Otu0001 1.241e-01
SM44 1 1 Bacteroides.Otu0001 5.478e-04
SM45 patient FALSE . 2 Bacteroides.Otu0001 0.000e+00
SM48 1 1 Bacteroides.Otu0001 6.268e-02
SM49 patient TRUE . 1 Bacteroides.Otu0001 1.179e-01
SM5 patient TRUE . 3 Bacteroides.Otu0001 2.741e-01
SM50 patient FALSE . 3 Bacteroides.Otu0001 0.000e+00
SM51 patient TRUE . 4 Bacteroides.Otu0001 2.826e-01
SM52 patient FALSE . 1 Bacteroides.Otu0001 5.829e-02
SM53 patient TRUE . 2 Bacteroides.Otu0001 2.368e-01
SM54 patient TRUE . 3 Bacteroides.Otu0001 0.000e+00
SM55 1 1 Bacteroides.Otu0001 2.798e-02
SM56 patient TRUE . 2 Bacteroides.Otu0001 0.000e+00
SM57 patient TRUE . 1 Bacteroides.Otu0001 1.037e-01
SM58 patient FALSE . 2 Bacteroides.Otu0001 1.620e-04
SM59 patient FALSE . 3 Bacteroides.Otu0001 3.745e-03
SM60 patient TRUE . 3 Bacteroides.Otu0001 2.447e-01
SM62 patient TRUE . 1 Bacteroides.Otu0001 5.347e-01
SM63 1 1 Bacteroides.Otu0001 8.649e-02
SM64 patient TRUE . 2 Bacteroides.Otu0001 3.508e-01
SM65 patient TRUE . 3 Bacteroides.Otu0001 8.092e-02
SM66 1 1 Bacteroides.Otu0001 1.585e-01
SM67 patient TRUE . 4 Bacteroides.Otu0001 2.186e-01
SM68 patient FALSE . 4 Bacteroides.Otu0001 0.000e+00
SM69 patient TRUE . 4 Bacteroides.Otu0001 1.655e-01
SM7 1 1 Bacteroides.Otu0001 4.313e-02
SM70 1 1 Bacteroides.Otu0001 1.567e-02
SM71 patient TRUE . 3 Bacteroides.Otu0001 2.788e-01
SM72 1 1 Bacteroides.Otu0001 1.323e-03
SM73 patient FALSE . 1 Bacteroides.Otu0001 1.891e-01
SM74 1 2 Bacteroides.Otu0001 5.565e-02
SM75 patient FALSE . 3 Bacteroides.Otu0001 0.000e+00
SM76 1 1 Bacteroides.Otu0001 2.751e-02
SM77 patient TRUE . 2 Bacteroides.Otu0001 2.034e-01
SM79 patient FALSE . 2 Bacteroides.Otu0001 2.642e-02
SM8 patient FALSE . 1 Bacteroides.Otu0001 5.265e-02
SM81 1 1 Bacteroides.Otu0001 0.000e+00
SM82 patient TRUE . 4 Bacteroides.Otu0001 1.052e-02
SM83 patient TRUE . 1 Bacteroides.Otu0001 0.000e+00
SM84 patient TRUE . 1 Bacteroides.Otu0001 1.247e-01
SM86 patient TRUE . 2 Bacteroides.Otu0001 0.000e+00
SM87 patient TRUE . 1 Bacteroides.Otu0001 1.941e-01
SM88 patient TRUE . 2 Bacteroides.Otu0001 2.302e-02
SM89 1 1 Bacteroides.Otu0001 0.000e+00
SM9 patient FALSE . 2 Bacteroides.Otu0001 3.497e-02
SM90 patient FALSE . 2 Bacteroides.Otu0001 3.713e-02
SM91 patient TRUE . 3 Bacteroides.Otu0001 1.254e-01
SM92 patient FALSE . 3 Bacteroides.Otu0001 0.000e+00
SM93 patient TRUE . 1 Bacteroides.Otu0001 3.120e-01
SM95 1 1 Bacteroides.Otu0001 1.492e-01
SM96 patient FALSE . 1 Bacteroides.Otu0001 0.000e+00
SM98 patient FALSE . 3 Bacteroides.Otu0001 3.648e-02
SM99 patient FALSE . 3 Bacteroides.Otu0001 4.305e-02
SM1 patient TRUE . 1 Bacteroides.Otu2520 1.003e-01
SM10 patient TRUE . 3 Bacteroides.Otu2520 0.000e+00
SM100 patient TRUE . 4 Bacteroides.Otu2520 0.000e+00
SM11 patient TRUE . 2 Bacteroides.Otu2520 1.344e-01
SM12 patient TRUE . 1 Bacteroides.Otu2520 1.504e-01
SM13 patient FALSE . 1 Bacteroides.Otu2520 1.473e-02
SM14 patient FALSE . 1 Bacteroides.Otu2520 3.786e-04
SM15 1 1 Bacteroides.Otu2520 1.756e-01
SM16 patient FALSE . 4 Bacteroides.Otu2520 0.000e+00
SM17 patient TRUE . 1 Bacteroides.Otu2520 1.862e-02
SM18 patient FALSE . 2 Bacteroides.Otu2520 1.074e-02
SM19 patient FALSE . 2 Bacteroides.Otu2520 9.255e-04
SM2 patient FALSE . 1 Bacteroides.Otu2520 1.638e-01
SM20 1 1 Bacteroides.Otu2520 2.417e-01
SM21 patient FALSE . 1 Bacteroides.Otu2520 4.540e-03
SM22 patient TRUE . 1 Bacteroides.Otu2520 2.610e-02
SM23 patient TRUE . 2 Bacteroides.Otu2520 0.000e+00
SM24 patient FALSE . 1 Bacteroides.Otu2520 5.531e-03
SM25 patient FALSE . 4 Bacteroides.Otu2520 3.053e-01
SM26 1 1 Bacteroides.Otu2520 4.378e-02
SM28 1 1 Bacteroides.Otu2520 0.000e+00
SM29 patient TRUE . 3 Bacteroides.Otu2520 0.000e+00
SM3 patient TRUE . 2 Bacteroides.Otu2520 5.657e-04
SM30 patient TRUE . 4 Bacteroides.Otu2520 3.250e-04
SM31 1 2 Bacteroides.Otu2520 1.173e-02
SM33 patient TRUE . 1 Bacteroides.Otu2520 7.120e-02
SM35 1 1 Bacteroides.Otu2520 1.330e-01
SM36 patient FALSE . 4 Bacteroides.Otu2520 0.000e+00
SM37 1 1 Bacteroides.Otu2520 3.158e-02
SM38 patient TRUE . 2 Bacteroides.Otu2520 9.696e-02
SM39 patient FALSE . 1 Bacteroides.Otu2520 8.620e-03
SM40 patient FALSE . 4 Bacteroides.Otu2520 5.920e-02
SM41 patient TRUE . 1 Bacteroides.Otu2520 1.440e-01
SM42 patient FALSE . 4 Bacteroides.Otu2520 1.665e-04
SM43 patient TRUE . 4 Bacteroides.Otu2520 3.957e-02
SM44 1 1 Bacteroides.Otu2520 1.369e-03
SM45 patient FALSE . 2 Bacteroides.Otu2520 0.000e+00
SM48 1 1 Bacteroides.Otu2520 1.951e-02
SM49 patient TRUE . 1 Bacteroides.Otu2520 1.715e-01
SM5 patient TRUE . 3 Bacteroides.Otu2520 0.000e+00
SM50 patient FALSE . 3 Bacteroides.Otu2520 0.000e+00
SM51 patient TRUE . 4 Bacteroides.Otu2520 3.368e-02
SM52 patient FALSE . 1 Bacteroides.Otu2520 2.179e-04
SM53 patient TRUE . 2 Bacteroides.Otu2520 7.192e-05
SM54 patient TRUE . 3 Bacteroides.Otu2520 2.426e-01
SM55 1 1 Bacteroides.Otu2520 1.289e-03
SM56 patient TRUE . 2 Bacteroides.Otu2520 9.465e-03
SM57 patient TRUE . 1 Bacteroides.Otu2520 0.000e+00
SM58 patient FALSE . 2 Bacteroides.Otu2520 3.239e-04
SM59 patient FALSE . 3 Bacteroides.Otu2520 2.996e-03
SM60 patient TRUE . 3 Bacteroides.Otu2520 5.548e-02
SM62 patient TRUE . 1 Bacteroides.Otu2520 1.525e-02
SM63 1 1 Bacteroides.Otu2520 4.324e-02
SM64 patient TRUE . 2 Bacteroides.Otu2520 9.297e-03
SM65 patient TRUE . 3 Bacteroides.Otu2520 0.000e+00
SM66 1 1 Bacteroides.Otu2520 9.282e-02
SM67 patient TRUE . 4 Bacteroides.Otu2520 0.000e+00
SM68 patient FALSE . 4 Bacteroides.Otu2520 0.000e+00
SM69 patient TRUE . 4 Bacteroides.Otu2520 1.197e-02
SM7 1 1 Bacteroides.Otu2520 0.000e+00
SM70 1 1 Bacteroides.Otu2520 5.961e-03
SM71 patient TRUE . 3 Bacteroides.Otu2520 2.162e-02
SM72 1 1 Bacteroides.Otu2520 0.000e+00
SM73 patient FALSE . 1 Bacteroides.Otu2520 5.047e-04
SM74 1 2 Bacteroides.Otu2520 0.000e+00
SM75 patient FALSE . 3 Bacteroides.Otu2520 2.037e-03
SM76 1 1 Bacteroides.Otu2520 1.085e-02
SM77 patient TRUE . 2 Bacteroides.Otu2520 8.359e-02
SM79 patient FALSE . 2 Bacteroides.Otu2520 1.576e-02
SM8 patient FALSE . 1 Bacteroides.Otu2520 0.000e+00
SM81 1 1 Bacteroides.Otu2520 0.000e+00
SM82 patient TRUE . 4 Bacteroides.Otu2520 3.568e-01
SM83 patient TRUE . 1 Bacteroides.Otu2520 0.000e+00
SM84 patient TRUE . 1 Bacteroides.Otu2520 2.912e-03
SM86 patient TRUE . 2 Bacteroides.Otu2520 0.000e+00
SM87 patient TRUE . 1 Bacteroides.Otu2520 4.566e-02
SM88 patient TRUE . 2 Bacteroides.Otu2520 1.604e-01
SM89 1 1 Bacteroides.Otu2520 0.000e+00
SM9 patient FALSE . 2 Bacteroides.Otu2520 5.636e-02
SM90 patient FALSE . 2 Bacteroides.Otu2520 2.558e-02
SM91 patient TRUE . 3 Bacteroides.Otu2520 8.567e-02
SM92 patient FALSE . 3 Bacteroides.Otu2520 9.504e-03
SM93 patient TRUE . 1 Bacteroides.Otu2520 4.034e-04
SM95 1 1 Bacteroides.Otu2520 6.748e-02
SM96 patient FALSE . 1 Bacteroides.Otu2520 4.602e-01
SM98 patient FALSE . 3 Bacteroides.Otu2520 9.832e-04
SM99 patient FALSE . 3 Bacteroides.Otu2520 4.757e-04
SM1 patient TRUE . 1 Faecalibacterium.Otu0067 6.148e-03
SM10 patient TRUE . 3 Faecalibacterium.Otu0067 1.051e-01
SM100 patient TRUE . 4 Faecalibacterium.Otu0067 6.200e-02
SM11 patient TRUE . 2 Faecalibacterium.Otu0067 1.893e-02
SM12 patient TRUE . 1 Faecalibacterium.Otu0067 4.471e-03
SM13 patient FALSE . 1 Faecalibacterium.Otu0067 8.929e-04
SM14 patient FALSE . 1 Faecalibacterium.Otu0067 4.014e-02
SM15 1 1 Faecalibacterium.Otu0067 2.045e-02
SM16 patient FALSE . 4 Faecalibacterium.Otu0067 1.237e-01
SM17 patient TRUE . 1 Faecalibacterium.Otu0067 4.137e-04
SM18 patient FALSE . 2 Faecalibacterium.Otu0067 3.022e-03
SM19 patient FALSE . 2 Faecalibacterium.Otu0067 2.920e-01
SM2 patient FALSE . 1 Faecalibacterium.Otu0067 9.919e-04
SM20 1 1 Faecalibacterium.Otu0067 8.058e-04
SM21 patient FALSE . 1 Faecalibacterium.Otu0067 1.093e-02
SM22 patient TRUE . 1 Faecalibacterium.Otu0067 4.607e-03
SM23 patient TRUE . 2 Faecalibacterium.Otu0067 0.000e+00
SM24 patient FALSE . 1 Faecalibacterium.Otu0067 1.839e-02
SM25 patient FALSE . 4 Faecalibacterium.Otu0067 6.406e-02
SM26 1 1 Faecalibacterium.Otu0067 6.205e-03
SM28 1 1 Faecalibacterium.Otu0067 1.307e-01
SM29 patient TRUE . 3 Faecalibacterium.Otu0067 3.342e-03
SM3 patient TRUE . 2 Faecalibacterium.Otu0067 3.733e-03
SM30 patient TRUE . 4 Faecalibacterium.Otu0067 1.202e-02
SM31 1 2 Faecalibacterium.Otu0067 2.427e-03
SM33 patient TRUE . 1 Faecalibacterium.Otu0067 0.000e+00

(1.1.1.4.3.2.4.2.1.1.1) Widget 67. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Stacked Bar Chart. Data grouped by Sample.type.Drug.Before,visit. Click to see HTML widget file in full window: ./1.1.1.4.3.2.4.2.1.1.1-3236ebfe9d0Dynamic.Pivot.Table.html

(1.1.1.4.3.2.4.2.1.1.1) Widget 68. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Table Barchart. Data grouped by Sample.type.Drug.Before,visit. Click to see HTML widget file in full window: ./1.1.1.4.3.2.4.2.1.1.1-32327db687bDynamic.Pivot.Table.html

(1.1.1.4.3.2.4.2.1.1.1) Table 65. Summary table. Data grouped by Sample.type.Drug.Before,visit. Showing only 200 first rows. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.1.1.4.3.2.4.2.1.1.1-3236113f391.1.1.1.4.3.2.4.2.1.1.csv

feature Sample.type.Drug.Before visit mean sd median incidence
Bacteroides.Otu0001 1 1 5.373e-02 5.181e-02 4.124e-02 0.8889
Bacteroides.Otu0001 1 2 4.724e-02 1.189e-02 4.724e-02 1.0000
Bacteroides.Otu0001 patient FALSE . 1 6.313e-02 6.443e-02 5.547e-02 0.8000
Bacteroides.Otu0001 patient FALSE . 2 1.951e-02 1.813e-02 2.642e-02 0.8571
Bacteroides.Otu0001 patient FALSE . 3 1.388e-02 2.021e-02 1.873e-03 0.5000
Bacteroides.Otu0001 patient FALSE . 4 5.335e-02 1.044e-01 8.834e-03 0.5000
Bacteroides.Otu0001 patient TRUE . 1 1.580e-01 1.466e-01 1.247e-01 0.8462
Bacteroides.Otu0001 patient TRUE . 2 1.604e-01 1.285e-01 2.120e-01 0.8000
Bacteroides.Otu0001 patient TRUE . 3 1.382e-01 1.150e-01 1.135e-01 0.7500
Bacteroides.Otu0001 patient TRUE . 4 1.211e-01 1.081e-01 1.241e-01 1.0000
Bacteroides.Otu2520 1 1 4.824e-02 7.012e-02 1.518e-02 0.7222
Bacteroides.Otu2520 1 2 5.866e-03 8.295e-03 5.866e-03 0.5000
Bacteroides.Otu2520 patient FALSE . 1 6.585e-02 1.474e-01 5.035e-03 0.9000
Bacteroides.Otu2520 patient FALSE . 2 1.567e-02 2.031e-02 1.074e-02 0.8571
Bacteroides.Otu2520 patient FALSE . 3 2.666e-03 3.521e-03 1.510e-03 0.8333
Bacteroides.Otu2520 patient FALSE . 4 6.078e-02 1.221e-01 8.323e-05 0.5000
Bacteroides.Otu2520 patient TRUE . 1 5.741e-02 6.351e-02 2.610e-02 0.8462
Bacteroides.Otu2520 patient TRUE . 2 4.947e-02 6.314e-02 9.381e-03 0.8000
Bacteroides.Otu2520 patient TRUE . 3 5.067e-02 8.384e-02 1.081e-02 0.5000
Bacteroides.Otu2520 patient TRUE . 4 6.319e-02 1.305e-01 1.197e-02 0.7143
Faecalibacterium.Otu0067 1 1 2.757e-02 3.097e-02 2.053e-02 0.9444
Faecalibacterium.Otu0067 1 2 2.134e-02 2.675e-02 2.134e-02 1.0000
Faecalibacterium.Otu0067 patient FALSE . 1 2.447e-02 2.587e-02 1.503e-02 1.0000
Faecalibacterium.Otu0067 patient FALSE . 2 5.462e-02 1.055e-01 1.279e-02 0.8571
Faecalibacterium.Otu0067 patient FALSE . 3 1.630e-02 1.924e-02 6.763e-03 0.8333
Faecalibacterium.Otu0067 patient FALSE . 4 7.234e-02 7.795e-02 4.539e-02 1.0000
Faecalibacterium.Otu0067 patient TRUE . 1 1.246e-02 1.071e-02 6.632e-03 0.9231
Faecalibacterium.Otu0067 patient TRUE . 2 3.949e-02 8.710e-02 7.349e-03 0.9000
Faecalibacterium.Otu0067 patient TRUE . 3 2.944e-02 3.510e-02 1.759e-02 1.0000
Faecalibacterium.Otu0067 patient TRUE . 4 2.888e-02 3.115e-02 1.202e-02 1.0000
Prevotella.Otu1987 1 1 6.034e-02 1.115e-01 0.000e+00 0.3333
Prevotella.Otu1987 1 2 0.000e+00 0.000e+00 0.000e+00 0.0000
Prevotella.Otu1987 patient FALSE . 1 5.770e-02 1.480e-01 0.000e+00 0.4000
Prevotella.Otu1987 patient FALSE . 2 4.991e-02 1.044e-01 0.000e+00 0.4286
Prevotella.Otu1987 patient FALSE . 3 4.009e-02 9.820e-02 0.000e+00 0.1667
Prevotella.Otu1987 patient FALSE . 4 1.542e-05 3.776e-05 0.000e+00 0.1667
Prevotella.Otu1987 patient TRUE . 1 1.090e-02 2.911e-02 0.000e+00 0.1538
Prevotella.Otu1987 patient TRUE . 2 1.933e-02 5.966e-02 1.932e-05 0.5000
Prevotella.Otu1987 patient TRUE . 3 2.731e-03 7.630e-03 0.000e+00 0.2500
Prevotella.Otu1987 patient TRUE . 4 6.413e-05 1.136e-04 0.000e+00 0.4286
Bacteroides.Otu0848 1 1 1.065e-02 2.194e-02 1.240e-03 0.6667
Bacteroides.Otu0848 1 2 4.248e-03 6.007e-03 4.248e-03 0.5000
Bacteroides.Otu0848 patient FALSE . 1 1.707e-02 3.960e-02 5.907e-03 0.9000
Bacteroides.Otu0848 patient FALSE . 2 6.903e-03 9.725e-03 2.057e-03 0.8571
Bacteroides.Otu0848 patient FALSE . 3 9.123e-02 1.945e-01 1.966e-04 0.5000
Bacteroides.Otu0848 patient FALSE . 4 1.501e-02 3.540e-02 6.597e-04 0.8333
Bacteroides.Otu0848 patient TRUE . 1 2.671e-02 3.193e-02 1.120e-02 0.8462
Bacteroides.Otu0848 patient TRUE . 2 2.030e-02 2.948e-02 2.863e-03 0.7000
Bacteroides.Otu0848 patient TRUE . 3 6.052e-02 8.697e-02 1.592e-02 0.7500
Bacteroides.Otu0848 patient TRUE . 4 4.907e-02 7.147e-02 2.948e-02 0.8571
Bacteroides.Otu2038 1 1 1.297e-02 3.185e-02 2.747e-03 0.7778
Bacteroides.Otu2038 1 2 2.898e-03 2.382e-03 2.898e-03 1.0000
Bacteroides.Otu2038 patient FALSE . 1 3.474e-02 8.766e-02 2.137e-03 0.9000
Bacteroides.Otu2038 patient FALSE . 2 6.335e-03 1.328e-02 4.859e-04 0.7143
Bacteroides.Otu2038 patient FALSE . 3 5.785e-02 1.371e-01 2.261e-03 0.5000
Bacteroides.Otu2038 patient FALSE . 4 7.519e-02 1.129e-01 2.006e-02 0.5000
Bacteroides.Otu2038 patient TRUE . 1 1.968e-02 4.234e-02 6.590e-03 0.8462
Bacteroides.Otu2038 patient TRUE . 2 2.811e-02 5.453e-02 7.947e-03 0.8000
Bacteroides.Otu2038 patient TRUE . 3 8.787e-03 9.306e-03 7.237e-03 0.7500
Bacteroides.Otu2038 patient TRUE . 4 1.065e-02 1.773e-02 1.341e-03 0.8571
Parabacteroides.Otu1736 1 1 4.727e-03 5.893e-03 3.900e-03 0.8333
Parabacteroides.Otu1736 1 2 8.764e-03 5.913e-03 8.764e-03 1.0000
Parabacteroides.Otu1736 patient FALSE . 1 3.866e-03 6.134e-03 1.455e-04 0.6000
Parabacteroides.Otu1736 patient FALSE . 2 1.770e-02 4.604e-02 4.893e-04 0.5714
Parabacteroides.Otu1736 patient FALSE . 3 7.007e-03 1.493e-02 0.000e+00 0.3333
Parabacteroides.Otu1736 patient FALSE . 4 6.321e-04 1.017e-03 0.000e+00 0.3333
Parabacteroides.Otu1736 patient TRUE . 1 4.142e-02 1.317e-01 1.328e-04 0.5385
Parabacteroides.Otu1736 patient TRUE . 2 7.001e-02 2.108e-01 0.000e+00 0.4000
Parabacteroides.Otu1736 patient TRUE . 3 3.964e-02 6.146e-02 6.241e-03 0.6250
Parabacteroides.Otu1736 patient TRUE . 4 1.770e-03 3.510e-03 0.000e+00 0.4286
Bacteroides.Otu2654 1 1 5.269e-03 8.442e-03 5.437e-04 0.7222
Bacteroides.Otu2654 1 2 0.000e+00 0.000e+00 0.000e+00 0.0000
Bacteroides.Otu2654 patient FALSE . 1 7.257e-02 1.423e-01 2.235e-03 0.7000
Bacteroides.Otu2654 patient FALSE . 2 1.413e-03 1.664e-03 8.251e-04 0.7143
Bacteroides.Otu2654 patient FALSE . 3 1.527e-03 2.490e-03 2.610e-04 0.6667
Bacteroides.Otu2654 patient FALSE . 4 3.480e-03 7.820e-03 3.116e-04 0.5000
Bacteroides.Otu2654 patient TRUE . 1 2.880e-02 3.291e-02 1.159e-02 0.8462
Bacteroides.Otu2654 patient TRUE . 2 9.244e-03 1.863e-02 1.462e-03 0.6000
Bacteroides.Otu2654 patient TRUE . 3 1.201e-02 2.697e-02 4.610e-04 0.7500
Bacteroides.Otu2654 patient TRUE . 4 1.339e-02 1.949e-02 4.248e-03 1.0000
Bacteroides.Otu2065 1 1 7.046e-03 1.378e-02 0.000e+00 0.3333
Bacteroides.Otu2065 1 2 0.000e+00 0.000e+00 0.000e+00 0.0000
Bacteroides.Otu2065 patient FALSE . 1 2.137e-04 5.675e-04 0.000e+00 0.2000
Bacteroides.Otu2065 patient FALSE . 2 0.000e+00 0.000e+00 0.000e+00 0.0000
Bacteroides.Otu2065 patient FALSE . 3 0.000e+00 0.000e+00 0.000e+00 0.0000
Bacteroides.Otu2065 patient FALSE . 4 1.135e-02 2.779e-02 0.000e+00 0.1667
Bacteroides.Otu2065 patient TRUE . 1 3.720e-02 1.082e-01 0.000e+00 0.2308
Bacteroides.Otu2065 patient TRUE . 2 1.184e-02 3.571e-02 0.000e+00 0.4000
Bacteroides.Otu2065 patient TRUE . 3 6.869e-02 1.851e-01 0.000e+00 0.3750
Bacteroides.Otu2065 patient TRUE . 4 2.219e-02 3.637e-02 1.625e-04 0.5714
Bacteroides.Otu0863 1 1 7.645e-03 8.815e-03 6.083e-03 0.7778
Bacteroides.Otu0863 1 2 6.250e-02 8.839e-02 6.250e-02 0.5000
Bacteroides.Otu0863 patient FALSE . 1 4.444e-02 7.340e-02 2.085e-02 0.9000
Bacteroides.Otu0863 patient FALSE . 2 5.955e-03 1.395e-02 5.036e-04 0.7143
Bacteroides.Otu0863 patient FALSE . 3 2.915e-03 4.516e-03 0.000e+00 0.3333
Bacteroides.Otu0863 patient FALSE . 4 2.470e-03 5.525e-03 0.000e+00 0.3333
Bacteroides.Otu0863 patient TRUE . 1 2.294e-02 4.344e-02 3.300e-03 0.8462
Bacteroides.Otu0863 patient TRUE . 2 1.605e-02 4.328e-02 1.028e-04 0.5000
Bacteroides.Otu0863 patient TRUE . 3 6.975e-03 9.227e-03 3.995e-03 0.7500
Bacteroides.Otu0863 patient TRUE . 4 2.140e-02 3.827e-02 4.546e-03 0.8571
Bacteroides.Otu2431 1 1 1.752e-02 2.195e-02 6.948e-03 0.7222
Bacteroides.Otu2431 1 2 1.133e-02 1.602e-02 1.133e-02 0.5000
Bacteroides.Otu2431 patient FALSE . 1 1.081e-02 1.187e-02 4.203e-03 0.8000
Bacteroides.Otu2431 patient FALSE . 2 1.465e-02 2.101e-02 6.715e-04 0.7143
Bacteroides.Otu2431 patient FALSE . 3 1.118e-03 2.044e-03 4.916e-05 0.5000
Bacteroides.Otu2431 patient FALSE . 4 3.160e-02 4.926e-02 4.451e-03 0.6667
Bacteroides.Otu2431 patient TRUE . 1 1.916e-02 2.943e-02 1.437e-02 0.8462
Bacteroides.Otu2431 patient TRUE . 2 1.612e-02 1.948e-02 8.648e-03 0.8000
Bacteroides.Otu2431 patient TRUE . 3 1.666e-02 1.369e-02 1.653e-02 1.0000
Bacteroides.Otu2431 patient TRUE . 4 2.214e-02 2.310e-02 1.294e-02 0.8571
Bacteroides.Otu0929 1 1 7.901e-03 9.570e-03 4.583e-03 0.8333
Bacteroides.Otu0929 1 2 1.136e-03 6.813e-04 1.136e-03 1.0000
Bacteroides.Otu0929 patient FALSE . 1 1.419e-02 2.249e-02 3.571e-03 0.7000
Bacteroides.Otu0929 patient FALSE . 2 5.678e-03 6.433e-03 4.197e-03 0.5714
Bacteroides.Otu0929 patient FALSE . 3 2.064e-03 4.875e-03 0.000e+00 0.3333
Bacteroides.Otu0929 patient FALSE . 4 6.298e-03 9.798e-03 0.000e+00 0.3333
Bacteroides.Otu0929 patient TRUE . 1 2.972e-02 6.220e-02 3.724e-03 0.7692
Bacteroides.Otu0929 patient TRUE . 2 2.250e-02 2.533e-02 1.586e-02 0.8000
Bacteroides.Otu0929 patient TRUE . 3 2.530e-02 2.588e-02 2.134e-02 0.8750
Bacteroides.Otu0929 patient TRUE . 4 1.556e-02 1.545e-02 1.297e-02 0.8571
Bacteroides.Otu1201 1 1 3.699e-03 4.973e-03 2.154e-03 0.7222
Bacteroides.Otu1201 1 2 2.104e-02 2.975e-02 2.104e-02 0.5000
Bacteroides.Otu1201 patient FALSE . 1 9.266e-03 1.027e-02 6.962e-03 0.9000
Bacteroides.Otu1201 patient FALSE . 2 1.400e-03 2.361e-03 0.000e+00 0.4286
Bacteroides.Otu1201 patient FALSE . 3 1.982e-05 4.855e-05 0.000e+00 0.1667
Bacteroides.Otu1201 patient FALSE . 4 2.775e-04 6.797e-04 0.000e+00 0.1667
Bacteroides.Otu1201 patient TRUE . 1 2.465e-02 5.589e-02 4.831e-03 0.7692
Bacteroides.Otu1201 patient TRUE . 2 4.627e-03 6.232e-03 1.186e-03 0.8000
Bacteroides.Otu1201 patient TRUE . 3 1.252e-02 2.175e-02 1.190e-03 0.6250
Bacteroides.Otu1201 patient TRUE . 4 6.109e-02 1.443e-01 4.281e-04 0.7143
Bacteroides.Otu0786 1 1 1.213e-03 2.598e-03 0.000e+00 0.3333
Bacteroides.Otu0786 1 2 1.618e-03 2.288e-03 1.618e-03 0.5000
Bacteroides.Otu0786 patient FALSE . 1 3.901e-03 7.552e-03 6.537e-04 0.5000
Bacteroides.Otu0786 patient FALSE . 2 5.539e-02 1.216e-01 8.663e-03 0.7143
Bacteroides.Otu0786 patient FALSE . 3 1.427e-02 3.351e-02 0.000e+00 0.3333
Bacteroides.Otu0786 patient FALSE . 4 4.070e-03 9.969e-03 0.000e+00 0.1667
Bacteroides.Otu0786 patient TRUE . 1 2.109e-02 6.921e-02 0.000e+00 0.4615
Bacteroides.Otu0786 patient TRUE . 2 3.762e-03 9.941e-03 0.000e+00 0.3000
Bacteroides.Otu0786 patient TRUE . 3 9.254e-03 1.752e-02 0.000e+00 0.3750
Bacteroides.Otu0786 patient TRUE . 4 2.042e-02 4.935e-02 0.000e+00 0.4286
Alistipes.Otu2508 1 1 1.852e-02 2.951e-02 4.785e-03 0.6667
Alistipes.Otu2508 1 2 5.057e-02 7.151e-02 5.057e-02 0.5000
Alistipes.Otu2508 patient FALSE . 1 2.934e-02 6.749e-02 1.338e-03 0.5000
Alistipes.Otu2508 patient FALSE . 2 1.036e-02 1.801e-02 0.000e+00 0.2857
Alistipes.Otu2508 patient FALSE . 3 8.739e-04 2.141e-03 0.000e+00 0.1667
Alistipes.Otu2508 patient FALSE . 4 3.251e-03 7.923e-03 0.000e+00 0.3333
Alistipes.Otu2508 patient TRUE . 1 8.815e-03 1.571e-02 5.195e-04 0.5385
Alistipes.Otu2508 patient TRUE . 2 4.655e-03 6.600e-03 0.000e+00 0.4000
Alistipes.Otu2508 patient TRUE . 3 6.563e-03 1.417e-02 5.301e-05 0.5000
Alistipes.Otu2508 patient TRUE . 4 6.108e-03 1.163e-02 0.000e+00 0.4286
Bacteroides.Otu2625 1 1 6.692e-03 1.678e-02 6.631e-04 0.6667
Bacteroides.Otu2625 1 2 4.248e-03 6.007e-03 4.248e-03 0.5000
Bacteroides.Otu2625 patient FALSE . 1 1.130e-02 3.301e-02 3.196e-04 0.6000
Bacteroides.Otu2625 patient FALSE . 2 4.114e-03 1.088e-02 0.000e+00 0.1429
Bacteroides.Otu2625 patient FALSE . 3 1.035e-03 1.676e-03 1.189e-04 0.5000
Bacteroides.Otu2625 patient FALSE . 4 1.065e-02 2.457e-02 0.000e+00 0.3333
Bacteroides.Otu2625 patient TRUE . 1 2.583e-02 5.292e-02 1.212e-03 0.6923
Bacteroides.Otu2625 patient TRUE . 2 7.327e-03 1.297e-02 1.092e-03 0.7000
Bacteroides.Otu2625 patient TRUE . 3 3.090e-02 8.438e-02 0.000e+00 0.3750
Bacteroides.Otu2625 patient TRUE . 4 2.022e-03 3.918e-03 3.058e-05 0.5714
Lactobacillus.Otu1332 1 1 0.000e+00 0.000e+00 0.000e+00 0.0000
Lactobacillus.Otu1332 1 2 0.000e+00 0.000e+00 0.000e+00 0.0000
Lactobacillus.Otu1332 patient FALSE . 1 1.529e-04 2.881e-04 0.000e+00 0.3000
Lactobacillus.Otu1332 patient FALSE . 2 1.424e-01 3.769e-01 0.000e+00 0.1429
Lactobacillus.Otu1332 patient FALSE . 3 8.800e-04 1.909e-03 0.000e+00 0.3333
Lactobacillus.Otu1332 patient FALSE . 4 5.364e-05 1.314e-04 0.000e+00 0.1667
Lactobacillus.Otu1332 patient TRUE . 1 0.000e+00 0.000e+00 0.000e+00 0.0000
Lactobacillus.Otu1332 patient TRUE . 2 5.567e-06 1.761e-05 0.000e+00 0.1000
Lactobacillus.Otu1332 patient TRUE . 3 0.000e+00 0.000e+00 0.000e+00 0.0000
Lactobacillus.Otu1332 patient TRUE . 4 0.000e+00 0.000e+00 0.000e+00 0.0000
Blautia.Otu2475 1 1 1.814e-02 4.375e-02 7.955e-03 1.0000
Blautia.Otu2475 1 2 1.313e-02 1.800e-02 1.313e-02 1.0000
Blautia.Otu2475 patient FALSE . 1 9.586e-03 1.290e-02 3.590e-03 1.0000
Blautia.Otu2475 patient FALSE . 2 6.603e-03 1.016e-02 1.664e-03 0.8571
Blautia.Otu2475 patient FALSE . 3 2.577e-02 2.399e-02 2.091e-02 1.0000
Blautia.Otu2475 patient FALSE . 4 8.660e-03 8.216e-03 4.604e-03 1.0000
Blautia.Otu2475 patient TRUE . 1 4.266e-03 5.462e-03 1.372e-03 0.8462
Blautia.Otu2475 patient TRUE . 2 9.397e-03 1.485e-02 4.721e-03 0.8000
Blautia.Otu2475 patient TRUE . 3 9.117e-03 1.032e-02 6.525e-03 1.0000
Blautia.Otu2475 patient TRUE . 4 1.130e-02 1.660e-02 3.353e-03 1.0000
Clostridium_XI.Otu1804 1 1 8.144e-03 1.014e-02 5.866e-03 0.9444
Clostridium_XI.Otu1804 1 2 9.628e-03 6.752e-03 9.628e-03 1.0000
Clostridium_XI.Otu1804 patient FALSE . 1 2.111e-02 3.509e-02 3.397e-03 0.9000
Clostridium_XI.Otu1804 patient FALSE . 2 3.633e-03 5.261e-03 2.854e-03 0.5714
Clostridium_XI.Otu1804 patient FALSE . 3 3.741e-03 4.719e-03 2.250e-03 0.8333
Clostridium_XI.Otu1804 patient FALSE . 4 2.675e-02 4.629e-02 7.207e-03 1.0000
Clostridium_XI.Otu1804 patient TRUE . 1 4.942e-03 1.055e-02 1.655e-03 0.7692
Clostridium_XI.Otu1804 patient TRUE . 2 1.619e-02 4.365e-02 9.337e-04 0.9000
Clostridium_XI.Otu1804 patient TRUE . 3 7.790e-03 1.040e-02 1.934e-03 1.0000
Clostridium_XI.Otu1804 patient TRUE . 4 1.497e-02 1.884e-02 4.832e-03 1.0000
Bacteroides.Otu0069 1 1 6.746e-03 6.781e-03 4.877e-03 0.7778
Bacteroides.Otu0069 1 2 6.721e-03 2.068e-03 6.721e-03 1.0000
Bacteroides.Otu0069 patient FALSE . 1 6.064e-03 6.818e-03 3.453e-03 0.8000
Bacteroides.Otu0069 patient FALSE . 2 2.499e-03 2.575e-03 2.879e-03 0.7143
Bacteroides.Otu0069 patient FALSE . 3 9.949e-04 1.568e-03 3.745e-04 0.5000
Bacteroides.Otu0069 patient FALSE . 4 3.397e-03 7.176e-03 3.250e-04 0.5000
Bacteroides.Otu0069 patient TRUE . 1 2.030e-02 1.993e-02 1.628e-02 0.8462
Bacteroides.Otu0069 patient TRUE . 2 2.071e-02 1.572e-02 2.446e-02 0.8000
Bacteroides.Otu0069 patient TRUE . 3 1.868e-02 1.841e-02 1.250e-02 0.7500
Bacteroides.Otu0069 patient TRUE . 4 1.377e-02 1.356e-02 1.364e-02 0.8571

(1.1.1.4.3.2.4.2.1.1.1) Figure 207. Abundance. Data grouped by Sample.type.Drug.Before,visit. bar_stacked plot. Image file: plots/32350ea69d9.svg.

(1.1.1.4.3.2.4.2.1.1.1) Figure 208. Abundance. Data grouped by Sample.type.Drug.Before,visit. bar (sample mean) plot. Image file: plots/323166766bc.svg.

(1.1.1.4.3.2.4.2.1.1.1) Figure 209. Abundance. Data grouped by Sample.type.Drug.Before,visit. violin plot. Image file: plots/323c1fa290.svg.

(1.1.1.4.3.2.4.2.1.1.1) Figure 210. Abundance. Data grouped by Sample.type.Drug.Before,visit. boxplot plot. Image file: plots/32370fa40a8.svg.

(1.1.1.4.3.2.4.2.1.2) Abundance. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.1.1.4.3.2.4.2.1.2.1) Figure 211. Abundance. Data grouped by Sample.type.Drug.Before,visit. bar (sample mean) plot. Image file: plots/3234568e917.svg.

(1.1.1.4.3.2.4.2.1.2.1) Figure 212. Abundance. Data grouped by Sample.type.Drug.Before,visit. violin plot. Image file: plots/3235f856975.svg.

(1.1.1.4.3.2.4.2.1.2.1) Figure 213. Abundance. Data grouped by Sample.type.Drug.Before,visit. boxplot plot. Image file: plots/3234a33976c.svg.

(1.1.1.4.3.2.4.2.2) dodged plots. Iterating over orientation and, optionally, scaling
(1.1.1.4.3.2.4.2.2.1) Abundance. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.1.1.4.3.2.4.2.2.1.1) Figure 214. Abundance. Data grouped by Sample.type.Drug.Before,visit. bar (sample mean) plot. Image file: plots/3232e86f690.svg.

(1.1.1.4.3.2.4.2.2.1.1) Figure 215. Abundance. Data grouped by Sample.type.Drug.Before,visit. violin plot. Image file: plots/3233fde0be4.svg.

(1.1.1.4.3.2.4.2.2.1.1) Figure 216. Abundance. Data grouped by Sample.type.Drug.Before,visit. boxplot plot. Image file: plots/3233cedd066.svg.

(1.1.1.4.3.2.4.2.2.2) Abundance. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.1.1.4.3.2.4.2.2.2.1) Figure 217. Abundance. Data grouped by Sample.type.Drug.Before,visit. bar (sample mean) plot. Image file: plots/323610b30ba.svg.

(1.1.1.4.3.2.4.2.2.2.1) Figure 218. Abundance. Data grouped by Sample.type.Drug.Before,visit. violin plot. Image file: plots/3231f4d190d.svg.

(1.1.1.4.3.2.4.2.2.2.1) Figure 219. Abundance. Data grouped by Sample.type.Drug.Before,visit. boxplot plot. Image file: plots/3236d36efb2.svg.

(1.1.1.4.3.2.5) Grouping variables Drug.Before.Diet,Sample.type.1
(1.1.1.4.3.2.6) Iterating over Abundance. profile sorting order
(1.1.1.4.3.2.6.1) Abundance. profile sorting order: average abundance
(1.1.1.4.3.2.6.2) Iterating over dodged vs faceted bars

The same data are shown in multiple combinations of graphical representations. This is the same data, but each plot highlights slightly different aspects of it. It is not likely that you will need every plot - pick only what you need.

(1.1.1.4.3.2.6.2.1) faceted plots. Iterating over orientation and, optionally, scaling
(1.1.1.4.3.2.6.2.1.1) Abundance. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.1.1.4.3.2.6.2.1.1.0) Table 66. Data table used for plots. Data grouped by Drug.Before.Diet,Sample.type.1. Showing only 200 first rows. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.1.1.4.3.2.6.2.1.1.0-323618c1631.1.1.1.4.3.2.6.2.1.1.csv

.record.id Drug.Before.Diet Sample.type.1 feature Abundance
SM1 DrugBefore_YES patient.before.diet Bacteroides.Otu0001 3.325e-02
SM10 DrugBefore_YES patient.after.diet Bacteroides.Otu0001 0.000e+00
SM100 DrugBefore_YES patient.after.diet Bacteroides.Otu0001 7.692e-05
SM11 DrugBefore_YES patient.after.diet Bacteroides.Otu0001 2.280e-01
SM12 DrugBefore_YES patient.before.diet Bacteroides.Otu0001 2.363e-01
SM13 DrugBefore_NO patient.before.diet Bacteroides.Otu0001 2.143e-02
SM14 DrugBefore_NO patient.before.diet Bacteroides.Otu0001 0.000e+00
SM15 DrugBefore_YES control Bacteroides.Otu0001 3.935e-02
SM16 DrugBefore_NO patient.after.diet Bacteroides.Otu0001 3.835e-02
SM17 DrugBefore_YES patient.before.diet Bacteroides.Otu0001 1.738e-01
SM18 DrugBefore_NO patient.after.diet Bacteroides.Otu0001 1.343e-03
SM19 DrugBefore_NO patient.after.diet Bacteroides.Otu0001 3.656e-02
SM2 DrugBefore_NO patient.before.diet Bacteroides.Otu0001 7.129e-03
SM20 DrugBefore_NO control Bacteroides.Otu0001 5.936e-02
SM21 DrugBefore_NO patient.before.diet Bacteroides.Otu0001 9.063e-02
SM22 DrugBefore_YES patient.before.diet Bacteroides.Otu0001 1.800e-01
SM23 DrugBefore_YES patient.after.diet Bacteroides.Otu0001 2.207e-01
SM24 DrugBefore_NO patient.before.diet Bacteroides.Otu0001 6.084e-02
SM25 DrugBefore_NO patient.after.diet Bacteroides.Otu0001 0.000e+00
SM26 DrugBefore_NO control Bacteroides.Otu0001 5.819e-02
SM28 DrugBefore_NO control Bacteroides.Otu0001 1.415e-01
SM29 DrugBefore_YES patient.after.diet Bacteroides.Otu0001 1.015e-01
SM3 DrugBefore_YES patient.after.diet Bacteroides.Otu0001 5.679e-02
SM30 DrugBefore_YES patient.after.diet Bacteroides.Otu0001 4.615e-02
SM31 DrugBefore_NO control Bacteroides.Otu0001 3.883e-02
SM33 DrugBefore_YES patient.before.diet Bacteroides.Otu0001 0.000e+00
SM35 DrugBefore_NO control Bacteroides.Otu0001 1.546e-02
SM36 DrugBefore_NO patient.after.diet Bacteroides.Otu0001 0.000e+00
SM37 DrugBefore_NO control Bacteroides.Otu0001 8.035e-02
SM38 DrugBefore_YES patient.after.diet Bacteroides.Otu0001 2.849e-01
SM39 DrugBefore_NO patient.before.diet Bacteroides.Otu0001 1.512e-01
SM40 DrugBefore_NO patient.after.diet Bacteroides.Otu0001 1.767e-02
SM41 DrugBefore_YES patient.before.diet Bacteroides.Otu0001 4.380e-02
SM42 DrugBefore_NO patient.after.diet Bacteroides.Otu0001 2.641e-01
SM43 DrugBefore_YES patient.after.diet Bacteroides.Otu0001 1.241e-01
SM44 DrugBefore_NO control Bacteroides.Otu0001 5.478e-04
SM45 DrugBefore_NO patient.after.diet Bacteroides.Otu0001 0.000e+00
SM48 DrugBefore_NO control Bacteroides.Otu0001 6.268e-02
SM49 DrugBefore_YES patient.before.diet Bacteroides.Otu0001 1.179e-01
SM5 DrugBefore_YES patient.after.diet Bacteroides.Otu0001 2.741e-01
SM50 DrugBefore_NO patient.after.diet Bacteroides.Otu0001 0.000e+00
SM51 DrugBefore_YES patient.after.diet Bacteroides.Otu0001 2.826e-01
SM52 DrugBefore_NO patient.before.diet Bacteroides.Otu0001 5.829e-02
SM53 DrugBefore_YES patient.after.diet Bacteroides.Otu0001 2.368e-01
SM54 DrugBefore_YES patient.after.diet Bacteroides.Otu0001 0.000e+00
SM55 DrugBefore_NO control Bacteroides.Otu0001 2.798e-02
SM56 DrugBefore_YES patient.after.diet Bacteroides.Otu0001 0.000e+00
SM57 DrugBefore_YES patient.before.diet Bacteroides.Otu0001 1.037e-01
SM58 DrugBefore_NO patient.after.diet Bacteroides.Otu0001 1.620e-04
SM59 DrugBefore_NO patient.after.diet Bacteroides.Otu0001 3.745e-03
SM60 DrugBefore_YES patient.after.diet Bacteroides.Otu0001 2.447e-01
SM62 DrugBefore_YES patient.before.diet Bacteroides.Otu0001 5.347e-01
SM63 DrugBefore_NO control Bacteroides.Otu0001 8.649e-02
SM64 DrugBefore_YES patient.after.diet Bacteroides.Otu0001 3.508e-01
SM65 DrugBefore_YES patient.after.diet Bacteroides.Otu0001 8.092e-02
SM66 DrugBefore_NO control Bacteroides.Otu0001 1.585e-01
SM67 DrugBefore_YES patient.after.diet Bacteroides.Otu0001 2.186e-01
SM68 DrugBefore_NO patient.after.diet Bacteroides.Otu0001 0.000e+00
SM69 DrugBefore_YES patient.after.diet Bacteroides.Otu0001 1.655e-01
SM7 DrugBefore_NO control Bacteroides.Otu0001 4.313e-02
SM70 DrugBefore_NO control Bacteroides.Otu0001 1.567e-02
SM71 DrugBefore_YES patient.after.diet Bacteroides.Otu0001 2.788e-01
SM72 DrugBefore_NO control Bacteroides.Otu0001 1.323e-03
SM73 DrugBefore_NO patient.before.diet Bacteroides.Otu0001 1.891e-01
SM74 DrugBefore_NO control Bacteroides.Otu0001 5.565e-02
SM75 DrugBefore_NO patient.after.diet Bacteroides.Otu0001 0.000e+00
SM76 DrugBefore_NO control Bacteroides.Otu0001 2.751e-02
SM77 DrugBefore_YES patient.after.diet Bacteroides.Otu0001 2.034e-01
SM79 DrugBefore_NO patient.after.diet Bacteroides.Otu0001 2.642e-02
SM8 DrugBefore_NO patient.before.diet Bacteroides.Otu0001 5.265e-02
SM81 DrugBefore_NO control Bacteroides.Otu0001 0.000e+00
SM82 DrugBefore_YES patient.after.diet Bacteroides.Otu0001 1.052e-02
SM83 DrugBefore_YES patient.before.diet Bacteroides.Otu0001 0.000e+00
SM84 DrugBefore_YES patient.before.diet Bacteroides.Otu0001 1.247e-01
SM86 DrugBefore_YES patient.after.diet Bacteroides.Otu0001 0.000e+00
SM87 DrugBefore_YES patient.before.diet Bacteroides.Otu0001 1.941e-01
SM88 DrugBefore_YES patient.after.diet Bacteroides.Otu0001 2.302e-02
SM89 DrugBefore_NO control Bacteroides.Otu0001 0.000e+00
SM9 DrugBefore_NO patient.after.diet Bacteroides.Otu0001 3.497e-02
SM90 DrugBefore_NO patient.after.diet Bacteroides.Otu0001 3.713e-02
SM91 DrugBefore_YES patient.after.diet Bacteroides.Otu0001 1.254e-01
SM92 DrugBefore_NO patient.after.diet Bacteroides.Otu0001 0.000e+00
SM93 DrugBefore_YES patient.before.diet Bacteroides.Otu0001 3.120e-01
SM95 DrugBefore_NO control Bacteroides.Otu0001 1.492e-01
SM96 DrugBefore_NO patient.before.diet Bacteroides.Otu0001 0.000e+00
SM98 DrugBefore_NO patient.after.diet Bacteroides.Otu0001 3.648e-02
SM99 DrugBefore_NO patient.after.diet Bacteroides.Otu0001 4.305e-02
SM1 DrugBefore_YES patient.before.diet Bacteroides.Otu2520 1.003e-01
SM10 DrugBefore_YES patient.after.diet Bacteroides.Otu2520 0.000e+00
SM100 DrugBefore_YES patient.after.diet Bacteroides.Otu2520 0.000e+00
SM11 DrugBefore_YES patient.after.diet Bacteroides.Otu2520 1.344e-01
SM12 DrugBefore_YES patient.before.diet Bacteroides.Otu2520 1.504e-01
SM13 DrugBefore_NO patient.before.diet Bacteroides.Otu2520 1.473e-02
SM14 DrugBefore_NO patient.before.diet Bacteroides.Otu2520 3.786e-04
SM15 DrugBefore_YES control Bacteroides.Otu2520 1.756e-01
SM16 DrugBefore_NO patient.after.diet Bacteroides.Otu2520 0.000e+00
SM17 DrugBefore_YES patient.before.diet Bacteroides.Otu2520 1.862e-02
SM18 DrugBefore_NO patient.after.diet Bacteroides.Otu2520 1.074e-02
SM19 DrugBefore_NO patient.after.diet Bacteroides.Otu2520 9.255e-04
SM2 DrugBefore_NO patient.before.diet Bacteroides.Otu2520 1.638e-01
SM20 DrugBefore_NO control Bacteroides.Otu2520 2.417e-01
SM21 DrugBefore_NO patient.before.diet Bacteroides.Otu2520 4.540e-03
SM22 DrugBefore_YES patient.before.diet Bacteroides.Otu2520 2.610e-02
SM23 DrugBefore_YES patient.after.diet Bacteroides.Otu2520 0.000e+00
SM24 DrugBefore_NO patient.before.diet Bacteroides.Otu2520 5.531e-03
SM25 DrugBefore_NO patient.after.diet Bacteroides.Otu2520 3.053e-01
SM26 DrugBefore_NO control Bacteroides.Otu2520 4.378e-02
SM28 DrugBefore_NO control Bacteroides.Otu2520 0.000e+00
SM29 DrugBefore_YES patient.after.diet Bacteroides.Otu2520 0.000e+00
SM3 DrugBefore_YES patient.after.diet Bacteroides.Otu2520 5.657e-04
SM30 DrugBefore_YES patient.after.diet Bacteroides.Otu2520 3.250e-04
SM31 DrugBefore_NO control Bacteroides.Otu2520 1.173e-02
SM33 DrugBefore_YES patient.before.diet Bacteroides.Otu2520 7.120e-02
SM35 DrugBefore_NO control Bacteroides.Otu2520 1.330e-01
SM36 DrugBefore_NO patient.after.diet Bacteroides.Otu2520 0.000e+00
SM37 DrugBefore_NO control Bacteroides.Otu2520 3.158e-02
SM38 DrugBefore_YES patient.after.diet Bacteroides.Otu2520 9.696e-02
SM39 DrugBefore_NO patient.before.diet Bacteroides.Otu2520 8.620e-03
SM40 DrugBefore_NO patient.after.diet Bacteroides.Otu2520 5.920e-02
SM41 DrugBefore_YES patient.before.diet Bacteroides.Otu2520 1.440e-01
SM42 DrugBefore_NO patient.after.diet Bacteroides.Otu2520 1.665e-04
SM43 DrugBefore_YES patient.after.diet Bacteroides.Otu2520 3.957e-02
SM44 DrugBefore_NO control Bacteroides.Otu2520 1.369e-03
SM45 DrugBefore_NO patient.after.diet Bacteroides.Otu2520 0.000e+00
SM48 DrugBefore_NO control Bacteroides.Otu2520 1.951e-02
SM49 DrugBefore_YES patient.before.diet Bacteroides.Otu2520 1.715e-01
SM5 DrugBefore_YES patient.after.diet Bacteroides.Otu2520 0.000e+00
SM50 DrugBefore_NO patient.after.diet Bacteroides.Otu2520 0.000e+00
SM51 DrugBefore_YES patient.after.diet Bacteroides.Otu2520 3.368e-02
SM52 DrugBefore_NO patient.before.diet Bacteroides.Otu2520 2.179e-04
SM53 DrugBefore_YES patient.after.diet Bacteroides.Otu2520 7.192e-05
SM54 DrugBefore_YES patient.after.diet Bacteroides.Otu2520 2.426e-01
SM55 DrugBefore_NO control Bacteroides.Otu2520 1.289e-03
SM56 DrugBefore_YES patient.after.diet Bacteroides.Otu2520 9.465e-03
SM57 DrugBefore_YES patient.before.diet Bacteroides.Otu2520 0.000e+00
SM58 DrugBefore_NO patient.after.diet Bacteroides.Otu2520 3.239e-04
SM59 DrugBefore_NO patient.after.diet Bacteroides.Otu2520 2.996e-03
SM60 DrugBefore_YES patient.after.diet Bacteroides.Otu2520 5.548e-02
SM62 DrugBefore_YES patient.before.diet Bacteroides.Otu2520 1.525e-02
SM63 DrugBefore_NO control Bacteroides.Otu2520 4.324e-02
SM64 DrugBefore_YES patient.after.diet Bacteroides.Otu2520 9.297e-03
SM65 DrugBefore_YES patient.after.diet Bacteroides.Otu2520 0.000e+00
SM66 DrugBefore_NO control Bacteroides.Otu2520 9.282e-02
SM67 DrugBefore_YES patient.after.diet Bacteroides.Otu2520 0.000e+00
SM68 DrugBefore_NO patient.after.diet Bacteroides.Otu2520 0.000e+00
SM69 DrugBefore_YES patient.after.diet Bacteroides.Otu2520 1.197e-02
SM7 DrugBefore_NO control Bacteroides.Otu2520 0.000e+00
SM70 DrugBefore_NO control Bacteroides.Otu2520 5.961e-03
SM71 DrugBefore_YES patient.after.diet Bacteroides.Otu2520 2.162e-02
SM72 DrugBefore_NO control Bacteroides.Otu2520 0.000e+00
SM73 DrugBefore_NO patient.before.diet Bacteroides.Otu2520 5.047e-04
SM74 DrugBefore_NO control Bacteroides.Otu2520 0.000e+00
SM75 DrugBefore_NO patient.after.diet Bacteroides.Otu2520 2.037e-03
SM76 DrugBefore_NO control Bacteroides.Otu2520 1.085e-02
SM77 DrugBefore_YES patient.after.diet Bacteroides.Otu2520 8.359e-02
SM79 DrugBefore_NO patient.after.diet Bacteroides.Otu2520 1.576e-02
SM8 DrugBefore_NO patient.before.diet Bacteroides.Otu2520 0.000e+00
SM81 DrugBefore_NO control Bacteroides.Otu2520 0.000e+00
SM82 DrugBefore_YES patient.after.diet Bacteroides.Otu2520 3.568e-01
SM83 DrugBefore_YES patient.before.diet Bacteroides.Otu2520 0.000e+00
SM84 DrugBefore_YES patient.before.diet Bacteroides.Otu2520 2.912e-03
SM86 DrugBefore_YES patient.after.diet Bacteroides.Otu2520 0.000e+00
SM87 DrugBefore_YES patient.before.diet Bacteroides.Otu2520 4.566e-02
SM88 DrugBefore_YES patient.after.diet Bacteroides.Otu2520 1.604e-01
SM89 DrugBefore_NO control Bacteroides.Otu2520 0.000e+00
SM9 DrugBefore_NO patient.after.diet Bacteroides.Otu2520 5.636e-02
SM90 DrugBefore_NO patient.after.diet Bacteroides.Otu2520 2.558e-02
SM91 DrugBefore_YES patient.after.diet Bacteroides.Otu2520 8.567e-02
SM92 DrugBefore_NO patient.after.diet Bacteroides.Otu2520 9.504e-03
SM93 DrugBefore_YES patient.before.diet Bacteroides.Otu2520 4.034e-04
SM95 DrugBefore_NO control Bacteroides.Otu2520 6.748e-02
SM96 DrugBefore_NO patient.before.diet Bacteroides.Otu2520 4.602e-01
SM98 DrugBefore_NO patient.after.diet Bacteroides.Otu2520 9.832e-04
SM99 DrugBefore_NO patient.after.diet Bacteroides.Otu2520 4.757e-04
SM1 DrugBefore_YES patient.before.diet Faecalibacterium.Otu0067 6.148e-03
SM10 DrugBefore_YES patient.after.diet Faecalibacterium.Otu0067 1.051e-01
SM100 DrugBefore_YES patient.after.diet Faecalibacterium.Otu0067 6.200e-02
SM11 DrugBefore_YES patient.after.diet Faecalibacterium.Otu0067 1.893e-02
SM12 DrugBefore_YES patient.before.diet Faecalibacterium.Otu0067 4.471e-03
SM13 DrugBefore_NO patient.before.diet Faecalibacterium.Otu0067 8.929e-04
SM14 DrugBefore_NO patient.before.diet Faecalibacterium.Otu0067 4.014e-02
SM15 DrugBefore_YES control Faecalibacterium.Otu0067 2.045e-02
SM16 DrugBefore_NO patient.after.diet Faecalibacterium.Otu0067 1.237e-01
SM17 DrugBefore_YES patient.before.diet Faecalibacterium.Otu0067 4.137e-04
SM18 DrugBefore_NO patient.after.diet Faecalibacterium.Otu0067 3.022e-03
SM19 DrugBefore_NO patient.after.diet Faecalibacterium.Otu0067 2.920e-01
SM2 DrugBefore_NO patient.before.diet Faecalibacterium.Otu0067 9.919e-04
SM20 DrugBefore_NO control Faecalibacterium.Otu0067 8.058e-04
SM21 DrugBefore_NO patient.before.diet Faecalibacterium.Otu0067 1.093e-02
SM22 DrugBefore_YES patient.before.diet Faecalibacterium.Otu0067 4.607e-03
SM23 DrugBefore_YES patient.after.diet Faecalibacterium.Otu0067 0.000e+00
SM24 DrugBefore_NO patient.before.diet Faecalibacterium.Otu0067 1.839e-02
SM25 DrugBefore_NO patient.after.diet Faecalibacterium.Otu0067 6.406e-02
SM26 DrugBefore_NO control Faecalibacterium.Otu0067 6.205e-03
SM28 DrugBefore_NO control Faecalibacterium.Otu0067 1.307e-01
SM29 DrugBefore_YES patient.after.diet Faecalibacterium.Otu0067 3.342e-03
SM3 DrugBefore_YES patient.after.diet Faecalibacterium.Otu0067 3.733e-03
SM30 DrugBefore_YES patient.after.diet Faecalibacterium.Otu0067 1.202e-02
SM31 DrugBefore_NO control Faecalibacterium.Otu0067 2.427e-03
SM33 DrugBefore_YES patient.before.diet Faecalibacterium.Otu0067 0.000e+00

(1.1.1.4.3.2.6.2.1.1.1) Widget 69. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Stacked Bar Chart. Data grouped by Drug.Before.Diet,Sample.type.1. Click to see HTML widget file in full window: ./1.1.1.4.3.2.6.2.1.1.1-32322f4e2e7Dynamic.Pivot.Table.html

(1.1.1.4.3.2.6.2.1.1.1) Widget 70. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Table Barchart. Data grouped by Drug.Before.Diet,Sample.type.1. Click to see HTML widget file in full window: ./1.1.1.4.3.2.6.2.1.1.1-32347af5f1dDynamic.Pivot.Table.html

(1.1.1.4.3.2.6.2.1.1.1) Table 67. Summary table. Data grouped by Drug.Before.Diet,Sample.type.1. Showing only 200 first rows. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.1.1.4.3.2.6.2.1.1.1-32310708d9a.1.1.1.4.3.2.6.2.1.1.csv

feature Drug.Before.Diet Sample.type.1 mean sd median incidence
Bacteroides.Otu0001 DrugBefore_NO control 5.381e-02 5.036e-02 4.313e-02 0.89474
Bacteroides.Otu0001 DrugBefore_NO patient.after.diet 2.842e-02 5.964e-02 3.745e-03 0.63158
Bacteroides.Otu0001 DrugBefore_NO patient.before.diet 6.313e-02 6.443e-02 5.547e-02 0.80000
Bacteroides.Otu0001 DrugBefore_YES control 3.935e-02 NA 3.935e-02 1.00000
Bacteroides.Otu0001 DrugBefore_YES patient.after.diet 1.423e-01 1.151e-01 1.254e-01 0.84000
Bacteroides.Otu0001 DrugBefore_YES patient.before.diet 1.580e-01 1.466e-01 1.247e-01 0.84615
Bacteroides.Otu2520 DrugBefore_NO control 3.707e-02 6.175e-02 1.085e-02 0.68421
Bacteroides.Otu2520 DrugBefore_NO patient.after.diet 2.581e-02 7.007e-02 9.832e-04 0.73684
Bacteroides.Otu2520 DrugBefore_NO patient.before.diet 6.585e-02 1.474e-01 5.035e-03 0.90000
Bacteroides.Otu2520 DrugBefore_YES control 1.756e-01 NA 1.756e-01 1.00000
Bacteroides.Otu2520 DrugBefore_YES patient.after.diet 5.370e-02 8.854e-02 9.465e-03 0.68000
Bacteroides.Otu2520 DrugBefore_YES patient.before.diet 5.741e-02 6.351e-02 2.610e-02 0.84615
Faecalibacterium.Otu0067 DrugBefore_NO control 2.729e-02 3.077e-02 2.062e-02 0.94737
Faecalibacterium.Otu0067 DrugBefore_NO patient.after.diet 4.812e-02 7.779e-02 1.279e-02 0.89474
Faecalibacterium.Otu0067 DrugBefore_NO patient.before.diet 2.447e-02 2.587e-02 1.503e-02 1.00000
Faecalibacterium.Otu0067 DrugBefore_YES control 2.045e-02 NA 2.045e-02 1.00000
Faecalibacterium.Otu0067 DrugBefore_YES patient.after.diet 3.330e-02 5.893e-02 1.216e-02 0.96000
Faecalibacterium.Otu0067 DrugBefore_YES patient.before.diet 1.246e-02 1.071e-02 6.632e-03 0.92308
Prevotella.Otu1987 DrugBefore_NO control 5.716e-02 1.093e-01 0.000e+00 0.31579
Prevotella.Otu1987 DrugBefore_NO patient.after.diet 3.105e-02 8.246e-02 0.000e+00 0.26316
Prevotella.Otu1987 DrugBefore_NO patient.before.diet 5.770e-02 1.480e-01 0.000e+00 0.40000
Prevotella.Otu1987 DrugBefore_YES control 0.000e+00 NA 0.000e+00 0.00000
Prevotella.Otu1987 DrugBefore_YES patient.after.diet 8.624e-03 3.785e-02 0.000e+00 0.40000
Prevotella.Otu1987 DrugBefore_YES patient.before.diet 1.090e-02 2.911e-02 0.000e+00 0.15385
Bacteroides.Otu0848 DrugBefore_NO control 1.047e-02 2.136e-02 1.277e-03 0.63158
Bacteroides.Otu0848 DrugBefore_NO patient.after.diet 3.609e-02 1.113e-01 8.098e-04 0.73684
Bacteroides.Otu0848 DrugBefore_NO patient.before.diet 1.707e-02 3.960e-02 5.907e-03 0.90000
Bacteroides.Otu0848 DrugBefore_YES control 1.203e-03 NA 1.203e-03 1.00000
Bacteroides.Otu0848 DrugBefore_YES patient.after.diet 4.123e-02 6.429e-02 1.414e-02 0.76000
Bacteroides.Otu0848 DrugBefore_YES patient.before.diet 2.671e-02 3.193e-02 1.120e-02 0.84615
Bacteroides.Otu2038 DrugBefore_NO control 1.092e-02 3.075e-02 2.708e-03 0.78947
Bacteroides.Otu2038 DrugBefore_NO patient.after.diet 4.435e-02 9.880e-02 4.859e-04 0.57895
Bacteroides.Otu2038 DrugBefore_NO patient.before.diet 3.474e-02 8.766e-02 2.137e-03 0.90000
Bacteroides.Otu2038 DrugBefore_YES control 3.177e-02 NA 3.177e-02 1.00000
Bacteroides.Otu2038 DrugBefore_YES patient.after.diet 1.704e-02 3.612e-02 5.176e-03 0.80000
Bacteroides.Otu2038 DrugBefore_YES patient.before.diet 1.968e-02 4.234e-02 6.590e-03 0.84615
Parabacteroides.Otu1736 DrugBefore_NO control 5.401e-03 5.902e-03 4.641e-03 0.89474
Parabacteroides.Otu1736 DrugBefore_NO patient.after.diet 8.934e-03 2.869e-02 0.000e+00 0.42105
Parabacteroides.Otu1736 DrugBefore_NO patient.before.diet 3.866e-03 6.134e-03 1.455e-04 0.60000
Parabacteroides.Otu1736 DrugBefore_YES control 0.000e+00 NA 0.000e+00 0.00000
Parabacteroides.Otu1736 DrugBefore_YES patient.after.diet 4.118e-02 1.363e-01 0.000e+00 0.48000
Parabacteroides.Otu1736 DrugBefore_YES patient.before.diet 4.142e-02 1.317e-01 1.328e-04 0.53846
Bacteroides.Otu2654 DrugBefore_NO control 4.958e-03 8.312e-03 2.739e-04 0.63158
Bacteroides.Otu2654 DrugBefore_NO patient.after.diet 2.101e-03 4.534e-03 5.872e-04 0.63158
Bacteroides.Otu2654 DrugBefore_NO patient.before.diet 7.257e-02 1.423e-01 2.235e-03 0.70000
Bacteroides.Otu2654 DrugBefore_YES control 6.369e-04 NA 6.369e-04 1.00000
Bacteroides.Otu2654 DrugBefore_YES patient.after.diet 1.129e-02 2.099e-02 7.919e-04 0.76000
Bacteroides.Otu2654 DrugBefore_YES patient.before.diet 2.880e-02 3.291e-02 1.159e-02 0.84615
Bacteroides.Otu2065 DrugBefore_NO control 6.675e-03 1.349e-02 0.000e+00 0.31579
Bacteroides.Otu2065 DrugBefore_NO patient.after.diet 3.583e-03 1.562e-02 0.000e+00 0.05263
Bacteroides.Otu2065 DrugBefore_NO patient.before.diet 2.137e-04 5.675e-04 0.000e+00 0.20000
Bacteroides.Otu2065 DrugBefore_YES control 0.000e+00 NA 0.000e+00 0.00000
Bacteroides.Otu2065 DrugBefore_YES patient.after.diet 3.293e-02 1.070e-01 0.000e+00 0.44000
Bacteroides.Otu2065 DrugBefore_YES patient.before.diet 3.720e-02 1.082e-01 0.000e+00 0.23077
Bacteroides.Otu0863 DrugBefore_NO control 1.236e-02 2.821e-02 5.201e-03 0.73684
Bacteroides.Otu0863 DrugBefore_NO patient.after.diet 3.895e-03 9.035e-03 0.000e+00 0.47368
Bacteroides.Otu0863 DrugBefore_NO patient.before.diet 4.444e-02 7.340e-02 2.085e-02 0.90000
Bacteroides.Otu0863 DrugBefore_YES control 2.774e-02 NA 2.774e-02 1.00000
Bacteroides.Otu0863 DrugBefore_YES patient.after.diet 1.464e-02 3.357e-02 1.507e-03 0.68000
Bacteroides.Otu0863 DrugBefore_YES patient.before.diet 2.294e-02 4.344e-02 3.300e-03 0.84615
Bacteroides.Otu2431 DrugBefore_NO control 1.621e-02 2.152e-02 2.708e-03 0.68421
Bacteroides.Otu2431 DrugBefore_NO patient.after.diet 1.573e-02 3.127e-02 3.915e-04 0.63158
Bacteroides.Otu2431 DrugBefore_NO patient.before.diet 1.081e-02 1.187e-02 4.203e-03 0.80000
Bacteroides.Otu2431 DrugBefore_YES control 2.993e-02 NA 2.993e-02 1.00000
Bacteroides.Otu2431 DrugBefore_YES patient.after.diet 1.798e-02 1.837e-02 1.615e-02 0.88000
Bacteroides.Otu2431 DrugBefore_YES patient.before.diet 1.916e-02 2.943e-02 1.437e-02 0.84615
Bacteroides.Otu0929 DrugBefore_NO control 6.163e-03 8.205e-03 1.676e-03 0.84211
Bacteroides.Otu0929 DrugBefore_NO patient.after.diet 4.733e-03 7.114e-03 0.000e+00 0.42105
Bacteroides.Otu0929 DrugBefore_NO patient.before.diet 1.419e-02 2.249e-02 3.571e-03 0.70000
Bacteroides.Otu0929 DrugBefore_YES control 2.739e-02 NA 2.739e-02 1.00000
Bacteroides.Otu0929 DrugBefore_YES patient.after.diet 2.145e-02 2.261e-02 1.848e-02 0.84000
Bacteroides.Otu0929 DrugBefore_YES patient.before.diet 2.972e-02 6.220e-02 3.724e-03 0.76923
Bacteroides.Otu1201 DrugBefore_NO control 5.544e-03 1.012e-02 1.858e-03 0.68421
Bacteroides.Otu1201 DrugBefore_NO patient.after.diet 6.098e-04 1.544e-03 0.000e+00 0.26316
Bacteroides.Otu1201 DrugBefore_NO patient.before.diet 9.266e-03 1.027e-02 6.962e-03 0.90000
Bacteroides.Otu1201 DrugBefore_YES control 3.326e-03 NA 3.326e-03 1.00000
Bacteroides.Otu1201 DrugBefore_YES patient.after.diet 2.296e-02 7.719e-02 1.130e-03 0.72000
Bacteroides.Otu1201 DrugBefore_YES patient.before.diet 2.465e-02 5.589e-02 4.831e-03 0.76923
Bacteroides.Otu0786 DrugBefore_NO control 1.290e-03 2.579e-03 0.000e+00 0.31579
Bacteroides.Otu0786 DrugBefore_NO patient.after.diet 2.620e-02 7.624e-02 0.000e+00 0.42105
Bacteroides.Otu0786 DrugBefore_NO patient.before.diet 3.901e-03 7.552e-03 6.537e-04 0.50000
Bacteroides.Otu0786 DrugBefore_YES control 5.661e-04 NA 5.661e-04 1.00000
Bacteroides.Otu0786 DrugBefore_YES patient.after.diet 1.018e-02 2.799e-02 0.000e+00 0.36000
Bacteroides.Otu0786 DrugBefore_YES patient.before.diet 2.109e-02 6.921e-02 0.000e+00 0.46154
Alistipes.Otu2508 DrugBefore_NO control 2.142e-02 3.474e-02 3.439e-03 0.63158
Alistipes.Otu2508 DrugBefore_NO patient.after.diet 5.120e-03 1.203e-02 0.000e+00 0.26316
Alistipes.Otu2508 DrugBefore_NO patient.before.diet 2.934e-02 6.749e-02 1.338e-03 0.50000
Alistipes.Otu2508 DrugBefore_YES control 2.753e-02 NA 2.753e-02 1.00000
Alistipes.Otu2508 DrugBefore_YES patient.after.diet 5.672e-03 1.046e-02 0.000e+00 0.44000
Alistipes.Otu2508 DrugBefore_YES patient.before.diet 8.815e-03 1.571e-02 5.195e-04 0.53846
Bacteroides.Otu2625 DrugBefore_NO control 6.746e-03 1.633e-02 5.478e-04 0.63158
Bacteroides.Otu2625 DrugBefore_NO patient.after.diet 5.204e-03 1.497e-02 0.000e+00 0.31579
Bacteroides.Otu2625 DrugBefore_NO patient.before.diet 1.130e-02 3.301e-02 3.196e-04 0.60000
Bacteroides.Otu2625 DrugBefore_YES control 7.784e-04 NA 7.784e-04 1.00000
Bacteroides.Otu2625 DrugBefore_YES patient.after.diet 1.338e-02 4.795e-02 2.263e-04 0.56000
Bacteroides.Otu2625 DrugBefore_YES patient.before.diet 2.583e-02 5.292e-02 1.212e-03 0.69231
Lactobacillus.Otu1332 DrugBefore_NO control 0.000e+00 0.000e+00 0.000e+00 0.00000
Lactobacillus.Otu1332 DrugBefore_NO patient.after.diet 5.277e-02 2.287e-01 0.000e+00 0.21053
Lactobacillus.Otu1332 DrugBefore_NO patient.before.diet 1.529e-04 2.881e-04 0.000e+00 0.30000
Lactobacillus.Otu1332 DrugBefore_YES control 0.000e+00 NA 0.000e+00 0.00000
Lactobacillus.Otu1332 DrugBefore_YES patient.after.diet 2.227e-06 1.113e-05 0.000e+00 0.04000
Lactobacillus.Otu1332 DrugBefore_YES patient.before.diet 0.000e+00 0.000e+00 0.000e+00 0.00000
Blautia.Otu2475 DrugBefore_NO control 1.783e-02 4.274e-02 6.667e-03 1.00000
Blautia.Otu2475 DrugBefore_NO patient.after.diet 1.331e-02 1.702e-02 4.670e-03 0.94737
Blautia.Otu2475 DrugBefore_NO patient.before.diet 9.586e-03 1.290e-02 3.590e-03 1.00000
Blautia.Otu2475 DrugBefore_YES control 1.401e-02 NA 1.401e-02 1.00000
Blautia.Otu2475 DrugBefore_YES patient.after.diet 9.839e-03 1.355e-02 3.353e-03 0.92000
Blautia.Otu2475 DrugBefore_YES patient.before.diet 4.266e-03 5.462e-03 1.372e-03 0.84615
Clostridium_XI.Otu1804 DrugBefore_NO control 8.215e-03 9.990e-03 5.737e-03 0.94737
Clostridium_XI.Otu1804 DrugBefore_NO patient.after.diet 1.097e-02 2.706e-02 3.230e-03 0.78947
Clostridium_XI.Otu1804 DrugBefore_NO patient.before.diet 2.111e-02 3.509e-02 3.397e-03 0.90000
Clostridium_XI.Otu1804 DrugBefore_YES control 9.766e-03 NA 9.766e-03 1.00000
Clostridium_XI.Otu1804 DrugBefore_YES patient.after.diet 1.316e-02 2.914e-02 2.507e-03 0.96000
Clostridium_XI.Otu1804 DrugBefore_YES patient.before.diet 4.942e-03 1.055e-02 1.655e-03 0.76923
Bacteroides.Otu0069 DrugBefore_NO control 6.781e-03 6.605e-03 5.259e-03 0.78947
Bacteroides.Otu0069 DrugBefore_NO patient.after.diet 2.308e-03 4.264e-03 6.500e-04 0.57895
Bacteroides.Otu0069 DrugBefore_NO patient.before.diet 6.064e-03 6.818e-03 3.453e-03 0.80000
Bacteroides.Otu0069 DrugBefore_YES control 6.015e-03 NA 6.015e-03 1.00000
Bacteroides.Otu0069 DrugBefore_YES patient.after.diet 1.811e-02 1.568e-02 1.785e-02 0.80000
Bacteroides.Otu0069 DrugBefore_YES patient.before.diet 2.030e-02 1.993e-02 1.628e-02 0.84615
Bacteroides.Otu2765 DrugBefore_NO control 4.484e-03 7.300e-03 1.022e-03 0.68421
Bacteroides.Otu2765 DrugBefore_NO patient.after.diet 1.074e-02 2.342e-02 6.391e-04 0.57895
Bacteroides.Otu2765 DrugBefore_NO patient.before.diet 8.715e-03 1.598e-02 3.269e-03 1.00000
Bacteroides.Otu2765 DrugBefore_YES control 1.486e-03 NA 1.486e-03 1.00000
Bacteroides.Otu2765 DrugBefore_YES patient.after.diet 1.449e-02 1.839e-02 6.915e-03 0.76000
Bacteroides.Otu2765 DrugBefore_YES patient.before.diet 1.573e-02 1.817e-02 8.930e-03 0.84615
Bacteroides.Otu0661 DrugBefore_NO control 5.940e-03 8.935e-03 2.023e-03 0.68421
Bacteroides.Otu0661 DrugBefore_NO patient.after.diet 3.711e-03 6.147e-03 0.000e+00 0.36842
Bacteroides.Otu0661 DrugBefore_NO patient.before.diet 1.512e-02 2.520e-02 2.777e-03 0.70000
Bacteroides.Otu0661 DrugBefore_YES control 2.180e-02 NA 2.180e-02 1.00000
Bacteroides.Otu0661 DrugBefore_YES patient.after.diet 1.493e-02 1.608e-02 8.012e-03 0.80000
Bacteroides.Otu0661 DrugBefore_YES patient.before.diet 1.291e-02 2.254e-02 3.919e-03 0.76923
Enterococcus.Otu1019 DrugBefore_NO control 3.316e-03 1.277e-02 0.000e+00 0.21053
Enterococcus.Otu1019 DrugBefore_NO patient.after.diet 2.710e-04 5.734e-04 0.000e+00 0.26316
Enterococcus.Otu1019 DrugBefore_NO patient.before.diet 7.372e-03 2.264e-02 0.000e+00 0.40000
Enterococcus.Otu1019 DrugBefore_YES control 0.000e+00 NA 0.000e+00 0.00000
Enterococcus.Otu1019 DrugBefore_YES patient.after.diet 2.867e-02 1.419e-01 0.000e+00 0.32000
Enterococcus.Otu1019 DrugBefore_YES patient.before.diet 2.860e-04 9.172e-04 0.000e+00 0.15385
Ruminococcus.Otu1859 DrugBefore_NO control 2.958e-02 5.475e-02 3.570e-03 0.68421
Ruminococcus.Otu1859 DrugBefore_NO patient.after.diet 4.938e-03 1.815e-02 0.000e+00 0.21053
Ruminococcus.Otu1859 DrugBefore_NO patient.before.diet 2.018e-04 6.381e-04 0.000e+00 0.10000
Ruminococcus.Otu1859 DrugBefore_YES control 1.395e-01 NA 1.395e-01 1.00000
Ruminococcus.Otu1859 DrugBefore_YES patient.after.diet 1.270e-04 3.390e-04 0.000e+00 0.20000
Ruminococcus.Otu1859 DrugBefore_YES patient.before.diet 2.526e-03 7.503e-03 0.000e+00 0.38462
Alistipes.Otu1466 DrugBefore_NO control 1.526e-02 3.931e-02 3.997e-04 0.52632
Alistipes.Otu1466 DrugBefore_NO patient.after.diet 4.484e-04 1.264e-03 0.000e+00 0.15789
Alistipes.Otu1466 DrugBefore_NO patient.before.diet 1.673e-02 2.486e-02 0.000e+00 0.40000
Alistipes.Otu1466 DrugBefore_YES control 1.741e-02 NA 1.741e-02 1.00000
Alistipes.Otu1466 DrugBefore_YES patient.after.diet 1.068e-02 3.068e-02 1.695e-04 0.52000
Alistipes.Otu1466 DrugBefore_YES patient.before.diet 6.337e-03 8.432e-03 3.106e-03 0.61538
Erysipelotrichaceae_incertae_sedis.Otu0818 DrugBefore_NO control 7.219e-04 1.301e-03 2.068e-04 0.52632
Erysipelotrichaceae_incertae_sedis.Otu0818 DrugBefore_NO patient.after.diet 1.463e-02 4.218e-02 3.329e-04 0.68421
Erysipelotrichaceae_incertae_sedis.Otu0818 DrugBefore_NO patient.before.diet 4.261e-02 1.209e-01 6.747e-04 0.70000
Erysipelotrichaceae_incertae_sedis.Otu0818 DrugBefore_YES control 1.415e-04 NA 1.415e-04 1.00000
Erysipelotrichaceae_incertae_sedis.Otu0818 DrugBefore_YES patient.after.diet 2.761e-03 5.093e-03 8.617e-04 1.00000
Erysipelotrichaceae_incertae_sedis.Otu0818 DrugBefore_YES patient.before.diet 2.499e-03 3.062e-03 1.373e-03 0.69231
Bacteroides.Otu0006 DrugBefore_NO control 4.531e-03 6.215e-03 2.798e-03 0.78947
Bacteroides.Otu0006 DrugBefore_NO patient.after.diet 6.412e-03 1.143e-02 1.679e-04 0.52632
Bacteroides.Otu0006 DrugBefore_NO patient.before.diet 8.986e-03 9.998e-03 5.553e-03 0.80000
Bacteroides.Otu0006 DrugBefore_YES control 8.634e-03 NA 8.634e-03 1.00000
Bacteroides.Otu0006 DrugBefore_YES patient.after.diet 1.377e-02 1.224e-02 9.732e-03 0.80000
Bacteroides.Otu0006 DrugBefore_YES patient.before.diet 1.169e-02 9.451e-03 1.076e-02 0.84615
Bacteroides.Otu2343 DrugBefore_NO control 7.244e-04 1.581e-03 0.000e+00 0.36842
Bacteroides.Otu2343 DrugBefore_NO patient.after.diet 1.707e-02 4.873e-02 0.000e+00 0.36842
Bacteroides.Otu2343 DrugBefore_NO patient.before.diet 2.821e-03 5.299e-03 3.268e-04 0.50000
Bacteroides.Otu2343 DrugBefore_YES control 2.123e-04 NA 2.123e-04 1.00000
Bacteroides.Otu2343 DrugBefore_YES patient.after.diet 8.282e-03 2.373e-02 0.000e+00 0.44000
Bacteroides.Otu2343 DrugBefore_YES patient.before.diet 1.169e-02 3.588e-02 4.426e-05 0.53846
Lachnospiracea_incertae_sedis.Otu0778 DrugBefore_NO control 2.272e-03 2.517e-03 1.761e-03 0.73684
Lachnospiracea_incertae_sedis.Otu0778 DrugBefore_NO patient.after.diet 2.327e-02 4.864e-02 2.063e-03 0.73684
Lachnospiracea_incertae_sedis.Otu0778 DrugBefore_NO patient.before.diet 1.746e-03 3.333e-03 5.304e-04 0.70000
Lachnospiracea_incertae_sedis.Otu0778 DrugBefore_YES control 1.698e-03 NA 1.698e-03 1.00000
Lachnospiracea_incertae_sedis.Otu0778 DrugBefore_YES patient.after.diet 6.888e-03 1.149e-02 8.631e-04 0.64000
Lachnospiracea_incertae_sedis.Otu0778 DrugBefore_YES patient.before.diet 1.864e-03 3.785e-03 0.000e+00 0.46154
Prevotella.Otu1633 DrugBefore_NO control 4.693e-03 1.082e-02 0.000e+00 0.42105
Prevotella.Otu1633 DrugBefore_NO patient.after.diet 2.517e-02 1.077e-01 0.000e+00 0.31579
Prevotella.Otu1633 DrugBefore_NO patient.before.diet 6.600e-03 1.426e-02 2.399e-04 0.70000
Prevotella.Otu1633 DrugBefore_YES control 0.000e+00 NA 0.000e+00 0.00000
Prevotella.Otu1633 DrugBefore_YES patient.after.diet 4.912e-04 2.061e-03 0.000e+00 0.20000
Prevotella.Otu1633 DrugBefore_YES patient.before.diet 3.413e-03 1.184e-02 0.000e+00 0.23077
Bacteroides.Otu2437 DrugBefore_NO control 1.182e-02 2.390e-02 7.937e-04 0.63158
Bacteroides.Otu2437 DrugBefore_NO patient.after.diet 9.308e-03 2.558e-02 0.000e+00 0.26316
Bacteroides.Otu2437 DrugBefore_NO patient.before.diet 3.138e-03 7.848e-03 3.035e-05 0.50000
Bacteroides.Otu2437 DrugBefore_YES control 7.077e-05 NA 7.077e-05 1.00000
Bacteroides.Otu2437 DrugBefore_YES patient.after.diet 7.334e-03 1.362e-02 0.000e+00 0.48000
Bacteroides.Otu2437 DrugBefore_YES patient.before.diet 2.995e-03 4.856e-03 0.000e+00 0.46154
Escherichia_Shigella.Otu2393 DrugBefore_NO control 9.648e-03 3.846e-02 3.570e-04 0.57895
Escherichia_Shigella.Otu2393 DrugBefore_NO patient.after.diet 9.277e-04 1.587e-03 8.323e-05 0.52632
Escherichia_Shigella.Otu2393 DrugBefore_NO patient.before.diet 1.334e-02 4.042e-02 6.431e-05 0.50000
Escherichia_Shigella.Otu2393 DrugBefore_YES control 0.000e+00 NA 0.000e+00 0.00000
Escherichia_Shigella.Otu2393 DrugBefore_YES patient.after.diet 4.697e-03 1.302e-02 0.000e+00 0.44000
Escherichia_Shigella.Otu2393 DrugBefore_YES patient.before.diet 1.464e-02 4.825e-02 0.000e+00 0.30769
Prevotella.Otu1994 DrugBefore_NO control 2.489e-02 5.887e-02 0.000e+00 0.21053
Prevotella.Otu1994 DrugBefore_NO patient.after.diet 0.000e+00 0.000e+00 0.000e+00 0.00000
Prevotella.Otu1994 DrugBefore_NO patient.before.diet 0.000e+00 0.000e+00 0.000e+00 0.00000
Prevotella.Otu1994 DrugBefore_YES control 0.000e+00 NA 0.000e+00 0.00000
Prevotella.Otu1994 DrugBefore_YES patient.after.diet 3.041e-03 1.382e-02 0.000e+00 0.16000
Prevotella.Otu1994 DrugBefore_YES patient.before.diet 5.947e-03 1.790e-02 0.000e+00 0.15385
Bacteroides.Otu0480 DrugBefore_NO control 1.342e-02 3.177e-02 0.000e+00 0.36842
Bacteroides.Otu0480 DrugBefore_NO patient.after.diet 2.327e-03 9.927e-03 0.000e+00 0.15789

(1.1.1.4.3.2.6.2.1.1.1) Figure 220. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. bar_stacked plot. Image file: plots/32369a21a37.svg.

(1.1.1.4.3.2.6.2.1.1.1) Figure 221. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. bar (sample mean) plot. Image file: plots/3236cd80714.svg.

(1.1.1.4.3.2.6.2.1.1.1) Figure 222. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. violin plot. Image file: plots/32367d78757.svg.

(1.1.1.4.3.2.6.2.1.1.1) Figure 223. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. boxplot plot. Image file: plots/32357a2f8fc.svg.

(1.1.1.4.3.2.6.2.1.2) Abundance. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.1.1.4.3.2.6.2.1.2.1) Figure 224. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. bar (sample mean) plot. Image file: plots/3233dc0a656.svg.

(1.1.1.4.3.2.6.2.1.2.1) Figure 225. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. violin plot. Image file: plots/3232dd99a77.svg.

(1.1.1.4.3.2.6.2.1.2.1) Figure 226. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. boxplot plot. Image file: plots/32314f7fdfa.svg.

(1.1.1.4.3.2.6.2.2) dodged plots. Iterating over orientation and, optionally, scaling
(1.1.1.4.3.2.6.2.2.1) Abundance. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.1.1.4.3.2.6.2.2.1.1) Figure 227. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. bar (sample mean) plot. Image file: plots/32321bc521d.svg.

(1.1.1.4.3.2.6.2.2.1.1) Figure 228. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. violin plot. Image file: plots/3237041014f.svg.

(1.1.1.4.3.2.6.2.2.1.1) Figure 229. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. boxplot plot. Image file: plots/3236b65b763.svg.

(1.1.1.4.3.2.6.2.2.2) Abundance. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.1.1.4.3.2.6.2.2.2.1) Figure 230. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. bar (sample mean) plot. Image file: plots/323725d871c.svg.

(1.1.1.4.3.2.6.2.2.2.1) Figure 231. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. violin plot. Image file: plots/3231c037676.svg.

(1.1.1.4.3.2.6.2.2.2.1) Figure 232. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. boxplot plot. Image file: plots/3236f20a731.svg.

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